Problem in calculating Depth of Coverage using GenomeAnalysisTK.jar

vishal666vishal666 KoelnPosts: 2Member

I am using this command to calculate the depth of coverage with three different formats for the EXOME_interval.list :
java -Xmx2048m -jar GenomeAnalysisTK.jar -T DepthOfCoverage -I /home/vsinha/software/bam/group1.READS.bam.list -L /home/vsinha/software/EXOME.interval_list -R /home/vsinha/software/human_g1k_v37.fasta -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o /home/vsinha/software/group1.DATA

1st format :
1 69114 69332
1 69383 69577
1 69644 69940
1 69951 70028
1 566170 566275
1 801895 801983
1 802332 802416
1 861272 861420

Error :
ERROR MESSAGE: Badly formed genome loc: Contig '1 69114 69332' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?

2nd format:
1:69114-69332
1:69383-69577
1:69644-69940
1:69951-70028
1:566170-566275
1:801895-801983
1:802332-802416
1:861272-861420

Error:
Badly formed genome loc: Contig '1' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?

3rd Format:
chr1:69114-69332
chr1:69383-69577
chr1:69644-69940
chr1:69951-70028
chr1:566170-566275
chr1:801895-801983
chr1:802332-802416
chr1:861272-861420

Error:
Contig chr1 not present in sequence dictionary for merged BAM header: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1]

Can you please let me know what is the problem in my file.

Thank You in advance.

Regards
Vishal

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    Hi Vishal,

    The second format you posted should be appropriate; I'm not sure why it's not going through. Have you tried specifying one contig using -L at the command-line, to see if that is recognized properly? Also, you can try deleting all index and dictionary files and re-generate them using Picard tools; maybe one of them is corrupt somehow.

    Geraldine Van der Auwera, PhD

  • tinutinu Posts: 44Member

    I am trying to make GVCF from a BAM and getting the same error. Reindexed and made new dictionaires for the fasta file

    **Error
    **##### ERROR MESSAGE: Contig 1 not present in sequence dictionary for merged BAM header: []

    **command **used
    java -Xmx4G -jarGenomeAnalysisTK.jar -T HaplotypeCaller -R /ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa -I SAMPLE1_reheader.bam -stand_call_conf 50 -stand_emit_conf 10.0 -L FINAL.processed.nochr.bed --variant_index_type LINEAR --variant_index_parameter 128000 --emitRefConfidence GVCF -o SAMPLE1_reheader.g.vcf

    **header of BAM
    **
    

    @HD VN:1.4 GO:none SO:coordinate
    @SQ 1 LN:249250621 AS:allchr.nix
    @SQ 2 LN:243199373 AS:allchr.nix
    @SQ 3 LN:198022430 AS:allchr.nix
    @SQ 4 LN:191154276 AS:allchr.nix
    @SQ 5 LN:180915260 AS:allchr.nix
    @SQ 6 LN:171115067 AS:allchr.nix
    @SQ 7 LN:159138663 AS:allchr.nix
    @SQ 8 LN:146364022 AS:allchr.nix
    @SQ 9 LN:141213431 AS:allchr.nix
    @SQ 10 LN:135534747 AS:allchr.nix
    @SQ 11 LN:135006516 AS:allchr.nix
    @SQ 12 LN:133851895 AS:allchr.nix
    @SQ 13 LN:115169878 AS:allchr.nix
    @SQ 14 LN:107349540 AS:allchr.nix
    @SQ 15 LN:102531392 AS:allchr.nix
    @SQ 16 LN:90354753 AS:allchr.nix
    @SQ 17 LN:81195210 AS:allchr.nix
    @SQ 18 LN:78077248 AS:allchr.nix
    @SQ 19 LN:59128983 AS:allchr.nix
    @SQ 20 LN:63025520 AS:allchr.nix
    @SQ 21 LN:48129895 AS:allchr.nix
    @SQ 22 LN:51304566 AS:allchr.nix
    @SQ X LN:155270560 AS:allchr.nix
    @SQ Y LN:59373566 AS:allchr.nix
    @SQ MT LN:16569 AS:allchr.nix
    @SQ GL000207.1 LN:4262 AS:allchr.nix
    @SQ GL000226.1 LN:15008 AS:allchr.nix
    @SQ GL000229.1 LN:19913 AS:allchr.nix
    @SQ GL000231.1 LN:27386 AS:allchr.nix
    @SQ GL000210.1 LN:27682 AS:allchr.nix
    @SQ GL000239.1 LN:33824 AS:allchr.nix
    @SQ GL000235.1 LN:34474 AS:allchr.nix
    @SQ GL000201.1 LN:36148 AS:allchr.nix
    @SQ GL000247.1 LN:36422 AS:allchr.nix
    @SQ GL000245.1 LN:36651 AS:allchr.nix
    @SQ GL000197.1 LN:37175 AS:allchr.nix
    @SQ GL000203.1 LN:37498 AS:allchr.nix
    @SQ GL000246.1 LN:38154 AS:allchr.nix
    @SQ GL000249.1 LN:38502 AS:allchr.nix
    @SQ GL000196.1 LN:38914 AS:allchr.nix
    @SQ GL000248.1 LN:39786 AS:allchr.nix
    @SQ GL000244.1 LN:39929 AS:allchr.nix
    @SQ GL000238.1 LN:39939 AS:allchr.nix
    @SQ GL000202.1 LN:40103 AS:allchr.nix
    @SQ GL000234.1 LN:40531 AS:allchr.nix
    @SQ GL000232.1 LN:40652 AS:allchr.nix
    @SQ GL000206.1 LN:41001 AS:allchr.nix
    @SQ GL000240.1 LN:41933 AS:allchr.nix
    @SQ GL000236.1 LN:41934 AS:allchr.nix
    @SQ GL000241.1 LN:42152 AS:allchr.nix
    @SQ GL000243.1 LN:43341 AS:allchr.nix
    @SQ GL000242.1 LN:43523 AS:allchr.nix
    @SQ GL000230.1 LN:43691 AS:allchr.nix
    @SQ GL000237.1 LN:45867 AS:allchr.nix
    @SQ GL000233.1 LN:45941 AS:allchr.nix
    @SQ GL000204.1 LN:81310 AS:allchr.nix
    @SQ GL000198.1 LN:90085 AS:allchr.nix
    @SQ GL000208.1 LN:92689 AS:allchr.nix
    @SQ GL000191.1 LN:106433 AS:allchr.nix
    @SQ GL000227.1 LN:128374 AS:allchr.nix
    @SQ GL000228.1 LN:129120 AS:allchr.nix
    @SQ GL000214.1 LN:137718 AS:allchr.nix
    @SQ GL000221.1 LN:155397 AS:allchr.nix
    @SQ GL000209.1 LN:159169 AS:allchr.nix
    @SQ GL000218.1 LN:161147 AS:allchr.nix
    @SQ GL000220.1 LN:161802 AS:allchr.nix
    @SQ GL000213.1 LN:164239 AS:allchr.nix
    @SQ GL000211.1 LN:166566 AS:allchr.nix
    @SQ GL000199.1 LN:169874 AS:allchr.nix
    @SQ GL000217.1 LN:172149 AS:allchr.nix
    @SQ GL000216.1 LN:172294 AS:allchr.nix
    @SQ GL000215.1 LN:172545 AS:allchr.nix
    @SQ GL000205.1 LN:174588 AS:allchr.nix
    @SQ GL000219.1 LN:179198 AS:allchr.nix
    @SQ GL000224.1 LN:179693 AS:allchr.nix
    @SQ GL000223.1 LN:180455 AS:allchr.nix
    @SQ GL000195.1 LN:182896 AS:allchr.nix
    @SQ GL000212.1 LN:186858 AS:allchr.nix
    @SQ GL000222.1 LN:186861 AS:allchr.nix
    @SQ GL000200.1 LN:187035 AS:allchr.nix
    @SQ GL000193.1 LN:189789 AS:allchr.nix
    @SQ GL000194.1 LN:191469 AS:allchr.nix
    @SQ GL000225.1 LN:211173 AS:allchr.nix
    @SQ GL000192.1 LN:547496 AS:allchr.nix

    **head FINAL.processed.nochr.bed
    **1 874546 875086 ABCA13
    1 1334072 1334252 AFMID
    1 1334309 1334845 AFMID
    1 1385068 1386190 ATAD3C
    1 1387229 1387769 AKNA
    1 1387373 1387553 ATAD3C
    1 1387689 1387869 ATAD3C
    1 1389682 1389922 ATAD3C
    1 1390779 1390959 ATAD3C
    1 1391113 1391353 ATAD3C

    **grep -P "^>" hs37d5.fa
    **>1 dna:chromosome chromosome:GRCh37:1:1:249250621:1

    2 dna:chromosome chromosome:GRCh37:2:1:243199373:1
    3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
    4 dna:chromosome chromosome:GRCh37:4:1:191154276:1
    5 dna:chromosome chromosome:GRCh37:5:1:180915260:1
    6 dna:chromosome chromosome:GRCh37:6:1:171115067:1
    7 dna:chromosome chromosome:GRCh37:7:1:159138663:1
    8 dna:chromosome chromosome:GRCh37:8:1:146364022:1
    9 dna:chromosome chromosome:GRCh37:9:1:141213431:1
    10 dna:chromosome chromosome:GRCh37:10:1:135534747:1
    11 dna:chromosome chromosome:GRCh37:11:1:135006516:1
    12 dna:chromosome chromosome:GRCh37:12:1:133851895:1
    13 dna:chromosome chromosome:GRCh37:13:1:115169878:1
    14 dna:chromosome chromosome:GRCh37:14:1:107349540:1
    15 dna:chromosome chromosome:GRCh37:15:1:102531392:1
    16 dna:chromosome chromosome:GRCh37:16:1:90354753:1
    17 dna:chromosome chromosome:GRCh37:17:1:81195210:1
    18 dna:chromosome chromosome:GRCh37:18:1:78077248:1
    19 dna:chromosome chromosome:GRCh37:19:1:59128983:1
    20 dna:chromosome chromosome:GRCh37:20:1:63025520:1
    21 dna:chromosome chromosome:GRCh37:21:1:48129895:1
    22 dna:chromosome chromosome:GRCh37:22:1:51304566:1
    X dna:chromosome chromosome:GRCh37:X:1:155270560:1
    Y dna:chromosome chromosome:GRCh37:Y:2649521:59034049:1
    MT gi|251831106|ref|NC_012920.1| Homo sapiens mitochondrion, complete genome
    GL000207.1 dna:supercontig supercontig::GL000207.1:1:4262:1
    GL000226.1 dna:supercontig supercontig::GL000226.1:1:15008:1
    GL000229.1 dna:supercontig supercontig::GL000229.1:1:19913:1
    GL000231.1 dna:supercontig supercontig::GL000231.1:1:27386:1
    GL000210.1 dna:supercontig supercontig::GL000210.1:1:27682:1
    GL000239.1 dna:supercontig supercontig::GL000239.1:1:33824:1
    GL000235.1 dna:supercontig supercontig::GL000235.1:1:34474:1
    GL000201.1 dna:supercontig supercontig::GL000201.1:1:36148:1
    GL000247.1 dna:supercontig supercontig::GL000247.1:1:36422:1
    GL000245.1 dna:supercontig supercontig::GL000245.1:1:36651:1
    GL000197.1 dna:supercontig supercontig::GL000197.1:1:37175:1
    GL000203.1 dna:supercontig supercontig::GL000203.1:1:37498:1
    GL000246.1 dna:supercontig supercontig::GL000246.1:1:38154:1
    GL000249.1 dna:supercontig supercontig::GL000249.1:1:38502:1
    GL000196.1 dna:supercontig supercontig::GL000196.1:1:38914:1
    GL000248.1 dna:supercontig supercontig::GL000248.1:1:39786:1
    GL000244.1 dna:supercontig supercontig::GL000244.1:1:39929:1
    GL000238.1 dna:supercontig supercontig::GL000238.1:1:39939:1
    GL000202.1 dna:supercontig supercontig::GL000202.1:1:40103:1
    GL000234.1 dna:supercontig supercontig::GL000234.1:1:40531:1
    GL000232.1 dna:supercontig supercontig::GL000232.1:1:40652:1
    GL000206.1 dna:supercontig supercontig::GL000206.1:1:41001:1
    GL000240.1 dna:supercontig supercontig::GL000240.1:1:41933:1
    GL000236.1 dna:supercontig supercontig::GL000236.1:1:41934:1
    GL000241.1 dna:supercontig supercontig::GL000241.1:1:42152:1
    GL000243.1 dna:supercontig supercontig::GL000243.1:1:43341:1
    GL000242.1 dna:supercontig supercontig::GL000242.1:1:43523:1
    GL000230.1 dna:supercontig supercontig::GL000230.1:1:43691:1
    GL000237.1 dna:supercontig supercontig::GL000237.1:1:45867:1
    GL000233.1 dna:supercontig supercontig::GL000233.1:1:45941:1
    GL000204.1 dna:supercontig supercontig::GL000204.1:1:81310:1
    GL000198.1 dna:supercontig supercontig::GL000198.1:1:90085:1
    GL000208.1 dna:supercontig supercontig::GL000208.1:1:92689:1
    GL000191.1 dna:supercontig supercontig::GL000191.1:1:106433:1
    GL000227.1 dna:supercontig supercontig::GL000227.1:1:128374:1
    GL000228.1 dna:supercontig supercontig::GL000228.1:1:129120:1
    GL000214.1 dna:supercontig supercontig::GL000214.1:1:137718:1
    GL000221.1 dna:supercontig supercontig::GL000221.1:1:155397:1
    GL000209.1 dna:supercontig supercontig::GL000209.1:1:159169:1
    GL000218.1 dna:supercontig supercontig::GL000218.1:1:161147:1
    GL000220.1 dna:supercontig supercontig::GL000220.1:1:161802:1
    GL000213.1 dna:supercontig supercontig::GL000213.1:1:164239:1
    GL000211.1 dna:supercontig supercontig::GL000211.1:1:166566:1
    GL000199.1 dna:supercontig supercontig::GL000199.1:1:169874:1
    GL000217.1 dna:supercontig supercontig::GL000217.1:1:172149:1
    GL000216.1 dna:supercontig supercontig::GL000216.1:1:172294:1
    GL000215.1 dna:supercontig supercontig::GL000215.1:1:172545:1
    GL000205.1 dna:supercontig supercontig::GL000205.1:1:174588:1
    GL000219.1 dna:supercontig supercontig::GL000219.1:1:179198:1
    GL000224.1 dna:supercontig supercontig::GL000224.1:1:179693:1
    GL000223.1 dna:supercontig supercontig::GL000223.1:1:180455:1
    GL000195.1 dna:supercontig supercontig::GL000195.1:1:182896:1
    GL000212.1 dna:supercontig supercontig::GL000212.1:1:186858:1
    GL000222.1 dna:supercontig supercontig::GL000222.1:1:186861:1
    GL000200.1 dna:supercontig supercontig::GL000200.1:1:187035:1
    GL000193.1 dna:supercontig supercontig::GL000193.1:1:189789:1
    GL000194.1 dna:supercontig supercontig::GL000194.1:1:191469:1
    GL000225.1 dna:supercontig supercontig::GL000225.1:1:211173:1
    GL000192.1 dna:supercontig supercontig::GL000192.1:1:547496:1
    NC_007605
    hs37d5

  • SheilaSheila Broad InstitutePosts: 1,648Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @tinu
    Hi,

    So, it looks like your bam file has a contig 1 in it. But, does you fasta dictionary file have contig 1 in it?

    -Sheila

  • tinutinu Posts: 44Member

    **yes, contigs in my fasta file

        1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
        2 dna:chromosome chromosome:GRCh37:2:1:243199373:1>3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
        4 dna:chromosome chromosome:GRCh37:4:1:191154276:1
        5 dna:chromosome chromosome:GRCh37:5:1:180915260:1
        6 dna:chromosome chromosome:GRCh37:6:1:171115067:1
        7 dna:chromosome chromosome:GRCh37:7:1:159138663:1
        8 dna:chromosome chromosome:GRCh37:8:1:146364022:1
        9 dna:chromosome chromosome:GRCh37:9:1:141213431:1
        10 dna:chromosome chromosome:GRCh37:10:1:135534747:1
        11 dna:chromosome chromosome:GRCh37:11:1:135006516:1
        12 dna:chromosome chromosome:GRCh37:12:1:133851895:1
        13 dna:chromosome chromosome:GRCh37:13:1:115169878:1
        14 dna:chromosome chromosome:GRCh37:14:1:107349540:1
        15 dna:chromosome chromosome:GRCh37:15:1:102531392:1
        16 dna:chromosome chromosome:GRCh37:16:1:90354753:1
        17 dna:chromosome chromosome:GRCh37:17:1:81195210:1
        18 dna:chromosome chromosome:GRCh37:18:1:78077248:1
        19 dna:chromosome chromosome:GRCh37:19:1:59128983:1
        20 dna:chromosome chromosome:GRCh37:20:1:63025520:1
        21 dna:chromosome chromosome:GRCh37:21:1:48129895:1
        22 dna:chromosome chromosome:GRCh37:22:1:51304566:1
        X dna:chromosome chromosome:GRCh37:X:1:155270560:1
        Y dna:chromosome chromosome:GRCh37:Y:2649521:59034049:1
        MT gi|251831106|ref|NC_012920.1| Homo sapiens mitochondrion, complete genome
        GL000207.1 dna:supercontig supercontig::GL000207.1:1:4262:1
        GL000226.1 dna:supercontig supercontig::GL000226.1:1:15008:1
        GL000229.1 dna:supercontig supercontig::GL000229.1:1:19913:1
        GL000231.1 dna:supercontig supercontig::GL000231.1:1:27386:1
        GL000210.1 dna:supercontig supercontig::GL000210.1:1:27682:1
        GL000239.1 dna:supercontig supercontig::GL000239.1:1:33824:1
        GL000235.1 dna:supercontig supercontig::GL000235.1:1:34474:1
        GL000201.1 dna:supercontig supercontig::GL000201.1:1:36148:1
        GL000247.1 dna:supercontig supercontig::GL000247.1:1:36422:1
        GL000245.1 dna:supercontig supercontig::GL000245.1:1:36651:1
        GL000197.1 dna:supercontig supercontig::GL000197.1:1:37175:1
        GL000203.1 dna:supercontig supercontig::GL000203.1:1:37498:1
        GL000246.1 dna:supercontig supercontig::GL000246.1:1:38154:1
        GL000249.1 dna:supercontig supercontig::GL000249.1:1:38502:1
        GL000196.1 dna:supercontig supercontig::GL000196.1:1:38914:1
        GL000248.1 dna:supercontig supercontig::GL000248.1:1:39786:1
        GL000244.1 dna:supercontig supercontig::GL000244.1:1:39929:1
        GL000238.1 dna:supercontig supercontig::GL000238.1:1:39939:1
        GL000202.1 dna:supercontig supercontig::GL000202.1:1:40103:1
        GL000234.1 dna:supercontig supercontig::GL000234.1:1:40531:1
        GL000232.1 dna:supercontig supercontig::GL000232.1:1:40652:1
        GL000206.1 dna:supercontig supercontig::GL000206.1:1:41001:1
        GL000240.1 dna:supercontig supercontig::GL000240.1:1:41933:1
        GL000236.1 dna:supercontig supercontig::GL000236.1:1:41934:1
        GL000241.1 dna:supercontig supercontig::GL000241.1:1:42152:1
        GL000243.1 dna:supercontig supercontig::GL000243.1:1:43341:1
        GL000242.1 dna:supercontig supercontig::GL000242.1:1:43523:1
        GL000230.1 dna:supercontig supercontig::GL000230.1:1:43691:1
        GL000237.1 dna:supercontig supercontig::GL000237.1:1:45867:1
        GL000233.1 dna:supercontig supercontig::GL000233.1:1:45941:1
        GL000204.1 dna:supercontig supercontig::GL000204.1:1:81310:1
        GL000198.1 dna:supercontig supercontig::GL000198.1:1:90085:1
        GL000208.1 dna:supercontig supercontig::GL000208.1:1:92689:1
        GL000191.1 dna:supercontig supercontig::GL000191.1:1:106433:1
        GL000227.1 dna:supercontig supercontig::GL000227.1:1:128374:1
        GL000228.1 dna:supercontig supercontig::GL000228.1:1:129120:1
        GL000214.1 dna:supercontig supercontig::GL000214.1:1:137718:1
        GL000221.1 dna:supercontig supercontig::GL000221.1:1:155397:1
        GL000209.1 dna:supercontig supercontig::GL000209.1:1:159169:1
        GL000218.1 dna:supercontig supercontig::GL000218.1:1:161147:1
        GL000220.1 dna:supercontig supercontig::GL000220.1:1:161802:1
        GL000213.1 dna:supercontig supercontig::GL000213.1:1:164239:1
        GL000211.1 dna:supercontig supercontig::GL000211.1:1:166566:1
        GL000199.1 dna:supercontig supercontig::GL000199.1:1:169874:1
        GL000217.1 dna:supercontig supercontig::GL000217.1:1:172149:1
        GL000216.1 dna:supercontig supercontig::GL000216.1:1:172294:1
        GL000215.1 dna:supercontig supercontig::GL000215.1:1:172545:1
        GL000205.1 dna:supercontig supercontig::GL000205.1:1:174588:1
        GL000219.1 dna:supercontig supercontig::GL000219.1:1:179198:1
        GL000224.1 dna:supercontig supercontig::GL000224.1:1:179693:1
        GL000223.1 dna:supercontig supercontig::GL000223.1:1:180455:1
        GL000195.1 dna:supercontig supercontig::GL000195.1:1:182896:1
        GL000212.1 dna:supercontig supercontig::GL000212.1:1:186858:1
        GL000222.1 dna:supercontig supercontig::GL000222.1:1:186861:1
        GL000200.1 dna:supercontig supercontig::GL000200.1:1:187035:1
        GL000193.1 dna:supercontig supercontig::GL000193.1:1:189789:1
        GL000194.1 dna:supercontig supercontig::GL000194.1:1:191469:1
        GL000225.1 dna:supercontig supercontig::GL000225.1:1:211173:1
        GL000192.1 dna:supercontig supercontig::GL000192.1:1:547496:1
        NC_007605
        hs37d5
        **
    
  • tinutinu Posts: 44Member

    Yes, fasta dictionary has it too

    @HD VN:1.4 SO:unsorted
    @SQ SN:1 LN:249250621 UR:file:/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa M5:1b22b98cdeb4a9304cb5d48026a85128
    @SQ SN:2 LN:243199373 UR:file:/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa M5:a0d9851da00400dec1098a9255ac712e
    @SQ SN:3 LN:198022430 UR:file:/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa M5:fdfd811849cc2fadebc929bb925902e5
    @SQ SN:4 LN:191154276 UR:file:/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa M5:23dccd106897542ad87d2765d28a19a1
    @SQ SN:5 LN:180915260 UR:file:/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa M5:0740173db9ffd264d728f32784845cd7
    @SQ SN:6 LN:171115067 UR:file:/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa M5:1d3a93a248d92a729ee764823acbbc6b
    @SQ SN:7 LN:159138663 UR:file:/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa M5:618366e953d6aaad97dbe4777c29375e
    @SQ SN:8 LN:146364022 UR:file:/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa M5:96f514a9929e410c6651697bded59aec
    @SQ SN:9 LN:141213431 UR:file:/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa M5:3e273117f15e0a400f01055d9f393768

  • SheilaSheila Broad InstitutePosts: 1,648Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @tinu
    Hi,

    Does your bam have multiple samples in it? It looks like you merged some bams. Does the command work on an unmerged bam? Perhaps one of the samples was not aligned to the same reference?

    -Sheila

  • tinutinu Posts: 44Member

    The bam file just have one sample

    Here is the RG tag information from the BAM

    @RG ID:s_10000223605__SCC_BCFR_NYC_FCCC_004A03_ PL:illumina PU:s_10000223605__SCC_BCFR_NYC_FCCC_004A03_ LB:hg19 SM:s_10000223605__SCC_BCFR_NYC_FCCC_004A03_ CN:mayo

  • SheilaSheila Broad InstitutePosts: 1,648Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @tinu
    Hi,

    Did you do a merge step on some bams to create your current bam? Can you explain exactly what you have done to the bam file before running Haplotype Caller?

    Thanks,
    Sheila

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