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The Splitting of BAM file (RNA-seq) before calling variants is throwing error

AlvaAlva SwitzerlandMember ✭✭

First of all I thank for the Tool , I am using this GATK var calling for my RNA-seq data.. I have been following the commands said in the site but its stopping me at the splitting BAM file step with the following error,

ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Badly formed genome loc: Contig * given as location, but this contig isn't present in the Fasta sequence dictionary

The command I used is,
/opt/husar/bin/java-1.7 -jar /GenomeAnalysisTK-3.2-2.jar -T SplitNCigarReads -R /human_genome37_gatk.fa -I BM_ID_reorder.bam -o BM_ID_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS

I tried do variant calling on the duplicate removed BAM file, which also throwed error message as,

ERROR
ERROR MESSAGE: SAM/BAM file BM_ID_reorder.bam is malformed: Reference index 1912602624 not found in sequence dictionary.
ERROR -

The command line I used for this,
/opt/husar/bin/java-1.7 -jar -Xincgc -Xmx1586M $NGSUTILDIR/java/GenomeAnalysisTK-3.2-2.jar -T HaplotypeCaller -R /human_genome37_gatk.fa -I BM_ID_reorder.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -stand_emit_conf 20.0 -o BM_ID.vcf

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Alva
    Hi,

    I think your issue can be fixed be running Picard's ReorderSam. http://broadinstitute.github.io/picard/command-line-overview.html#ReorderSam

    If that does not fix the issue, can you tell me what errors are thrown when you run Picard's ValidateSamFile? http://broadinstitute.github.io/picard/command-line-overview.html#ValidateSamFile

    Thanks,
    Sheila

  • AlvaAlva SwitzerlandMember ✭✭

    Hello Sheila,
    Thank you so much for your reply.!

    Yes I tried both reorderSam, and validatesamfile
    /opt/husar/bin/java-1.7 -jar /ReorderSam.jar I=BM_ID_dedupped.bam R=/human_genome37_gatk.fa O=BM_ID_reorder.bam

    and on that BAM file I have ran validateSamFile
    After running validatesamfile ,
    /opt/husar/bin/java-1.7 -jar --Xmx2g ValidateSamFile.jar I=BM_ID_reorder.bam
    I have the following error,
    ERROR: Invalid GZIP header
    This error I dont know how to resolve, it would be great if you would walk me a little bit more ..

    Thank you

  • AlvaAlva SwitzerlandMember ✭✭

    Hello All,
    I have tried validatesamfile with the following command
    /opt/husar/bin/java-1.7 -jar -Xincgc -Xmx1586M /nfs/gcg/husar.gcg10.2-centos-husar3/ngs/java/picard-tools-1.78/ValidateSamFile.jar I=BM_ID_reorder.bam MODE=SUMMARY

    and it gives me following report,
    No errors found
    and so then I ran ,
    java-1.7 -jar -Xincgc -Xmx1586M /GenomeAnalysisTK-3.2-2.jar -T SplitNCigarReads -R /gcg/husar/gcgdata/ngsdata/gatk/human_genome37_gatk.fa -I BM_ID_reorder.bam -o BM_ID_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS

    its throwing me the same error again,

    ERROR
    ERROR MESSAGE: Badly formed genome loc: Contig * given as location, but this contig isn't present in the Fasta sequence dictionary
    ERROR ------------------------------------------------------------------------------------------

    Any assistance would be great..!!!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Alva
    Hi,

    Now I am confused. Did you run ValidateSamFile on the same bam both times (in your previous post and this post)? And, did ValidateSamFile give errors in one run but not in the other? Or, did you fix the previous error then run ValidateSamFile?

    Can you post the .dict file? Also, please post the input bam header.

    Thanks,
    Sheila

  • AlvaAlva SwitzerlandMember ✭✭

    Ok, yeah I have fixed the error, I mean when I indexed the same BAM file and then did a validatesamFile check on it and so it gave me the current output as NO errors
    Can you post the .dict file? I am sorry i dont see such a file in my directory..
    Also, please post the input bam header.
    here is it looks like,
    @HD VN:1.4 SO:coordinate
    @SQ SN:chrM LN:16571 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb
    @SQ SN:chr1 LN:249250621 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1b22b98cdeb4a9304cb5d48026a85128
    @SQ SN:chr2 LN:243199373 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:a0d9851da00400dec1098a9255ac712e
    @SQ SN:chr3 LN:198022430 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:641e4338fa8d52a5b781bd2a2c08d3c3
    @SQ SN:chr4 LN:191154276 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:23dccd106897542ad87d2765d28a19a1
    @SQ SN:chr5 LN:180915260 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:0740173db9ffd264d728f32784845cd7
    @SQ SN:chr6 LN:171115067 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1d3a93a248d92a729ee764823acbbc6b
    @SQ SN:chr7 LN:159138663 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:618366e953d6aaad97dbe4777c29375e
    @SQ SN:chr8 LN:146364022 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:96f514a9929e410c6651697bded59aec
    @SQ SN:chr9 LN:141213431 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:3e273117f15e0a400f01055d9f393768
    @SQ SN:chr10 LN:135534747 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:988c28e000e84c26d552359af1ea2e1d
    @SQ SN:chr11 LN:135006516 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:98c59049a2df285c76ffb1c6db8f8b96
    @SQ SN:chr12 LN:133851895 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:51851ac0e1a115847ad36449b0015864
    @SQ SN:chr13 LN:115169878 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:283f8d7892baa81b510a015719ca7b0b
    @SQ SN:chr14 LN:107349540 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:98f3cae32b2a2e9524bc19813927542e
    @SQ SN:chr15 LN:102531392 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:e5645a794a8238215b2cd77acb95a078
    @SQ SN:chr16 LN:90354753 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:fc9b1a7b42b97a864f56b348b06095e6
    @SQ SN:chr17 LN:81195210 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:351f64d4f4f9ddd45b35336ad97aa6de
    @SQ SN:chr18 LN:78077248 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c
    @SQ SN:chr19 LN:59128983 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1aacd71f30db8e561810913e0b72636d
    @SQ SN:chr20 LN:63025520 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:0dec9660ec1efaaf33281c0d5ea2560f
    @SQ SN:chr21 LN:48129895 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:2979a6085bfe28e3ad6f552f361ed74d
    @SQ SN:chr22 LN:51304566 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:a718acaa6135fdca8357d5bfe94211dd
    @SQ SN:chrX LN:155270560 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:7e0e2e580297b7764e31dbc80c2540dd
    @SQ SN:chrY LN:59373566 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1e86411d73e6f00a10590f976be01623
    @SQ SN:chr1_gl000191_random LN:106433 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:d75b436f50a8214ee9c2a51d30b2c2cc
    @SQ SN:chr1_gl000192_random LN:547496 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:325ba9e808f669dfeee210fdd7b470ac
    @SQ SN:chr4_ctg9_hap1 LN:590426 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:fa24f81b680df26bcfb6d69b784fbe36
    @SQ SN:chr4_gl000193_random LN:189789 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:dbb6e8ece0b5de29da56601613007c2a
    @SQ SN:chr4_gl000194_random LN:191469 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:6ac8f815bf8e845bb3031b73f812c012
    @SQ SN:chr6_apd_hap1 LN:4622290 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:fe71bc63420d666884f37a3ad79f3317
    @SQ SN:chr6_cox_hap2 LN:4795371 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:18c17e1641ef04873b15f40f6c8659a4
    @SQ SN:chr6_dbb_hap3 LN:4610396 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:2a3c677c426a10e137883ae1ffb8da3f
    @SQ SN:chr6_mann_hap4 LN:4683263 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:9d51d4152174461cd6715c7ddc588dc8
    @SQ SN:chr6_mcf_hap5 LN:4833398 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:efed415dd8742349cb7aaca054675b9a
    @SQ SN:chr6_qbl_hap6 LN:4611984 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:094d037050cad692b57ea12c4fef790f
    @SQ SN:chr6_ssto_hap7 LN:4928567 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:3b6d666200e72bcc036bf88a4d7e0749
    @SQ SN:chr7_gl000195_random LN:182896 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:5d9ec007868d517e73543b005ba48535
    @SQ SN:chr8_gl000196_random LN:38914 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:d92206d1bb4c3b4019c43c0875c06dc0
    @SQ SN:chr8_gl000197_random LN:37175 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:6f5efdd36643a9b8c8ccad6f2f1edc7b
    @SQ SN:chr9_gl000198_random LN:90085 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:868e7784040da90d900d2d1b667a1383
    @SQ SN:chr9_gl000199_random LN:169874 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:569af3b73522fab4b40995ae4944e78e
    @SQ SN:chr9_gl000200_random LN:187035 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:75e4c8d17cd4addf3917d1703cacaf25
    @SQ SN:chr9_gl000201_random LN:36148 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:dfb7e7ec60ffdcb85cb359ea28454ee9
    @SQ SN:chr11_gl000202_random LN:40103 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:06cbf126247d89664a4faebad130fe9c
    @SQ SN:chr17_ctg5_hap1 LN:1680828 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:d89517b400226d3b56e753972a7cad67
    @SQ SN:chr17_gl000203_random LN:37498 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:96358c325fe0e70bee73436e8bb14dbd
    @SQ SN:chr17_gl000204_random LN:81310 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:efc49c871536fa8d79cb0a06fa739722
    @SQ SN:chr17_gl000205_random LN:174588 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:d22441398d99caf673e9afb9a1908ec5
    @SQ SN:chr17_gl000206_random LN:41001 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:43f69e423533e948bfae5ce1d45bd3f1
    @SQ SN:chr18_gl000207_random LN:4262 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:f3814841f1939d3ca19072d9e89f3fd7
    @SQ SN:chr19_gl000208_random LN:92689 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:aa81be49bf3fe63a79bdc6a6f279abf6
    @SQ SN:chr19_gl000209_random LN:159169 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:f40598e2a5a6b26e84a3775e0d1e2c81
    @SQ SN:chr21_gl000210_random LN:27682 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:851106a74238044126131ce2a8e5847c
    @SQ SN:chrUn_gl000211 LN:166566 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:7daaa45c66b288847b9b32b964e623d3
    @SQ SN:chrUn_gl000212 LN:186858 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:563531689f3dbd691331fd6c5730a88b
    @SQ SN:chrUn_gl000213 LN:164239 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:9d424fdcc98866650b58f004080a992a
    @SQ SN:chrUn_gl000214 LN:137718 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:46c2032c37f2ed899eb41c0473319a69
    @SQ SN:chrUn_gl000215 LN:172545 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:5eb3b418480ae67a997957c909375a73
    @SQ SN:chrUn_gl000216 LN:172294 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:642a232d91c486ac339263820aef7fe0
    @SQ SN:chrUn_gl000217 LN:172149 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:6d243e18dea1945fb7f2517615b8f52e
    @SQ SN:chrUn_gl000218 LN:161147 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1d708b54644c26c7e01c2dad5426d38c
    @SQ SN:chrUn_gl000219 LN:179198 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:f977edd13bac459cb2ed4a5457dba1b3
    @SQ SN:chrUn_gl000220 LN:161802 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:fc35de963c57bf7648429e6454f1c9db
    @SQ SN:chrUn_gl000221 LN:155397 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:3238fb74ea87ae857f9c7508d315babb
    @SQ SN:chrUn_gl000222 LN:186861 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:6fe9abac455169f50470f5a6b01d0f59
    @SQ SN:chrUn_gl000223 LN:180455 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:399dfa03bf32022ab52a846f7ca35b30
    @SQ SN:chrUn_gl000224 LN:179693 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:d5b2fc04f6b41b212a4198a07f450e20
    @SQ SN:chrUn_gl000225 LN:211173 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:63945c3e6962f28ffd469719a747e73c
    @SQ SN:chrUn_gl000226 LN:15008 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1c1b2cd1fccbc0a99b6a447fa24d1504
    @SQ SN:chrUn_gl000227 LN:128374 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:a4aead23f8053f2655e468bcc6ecdceb
    @SQ SN:chrUn_gl000228 LN:129120 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:c5a17c97e2c1a0b6a9cc5a6b064b714f
    @SQ SN:chrUn_gl000229 LN:19913 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:d0f40ec87de311d8e715b52e4c7062e1
    @SQ SN:chrUn_gl000230 LN:43691 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:b4eb71ee878d3706246b7c1dbef69299
    @SQ SN:chrUn_gl000231 LN:27386 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:ba8882ce3a1efa2080e5d29b956568a4
    @SQ SN:chrUn_gl000232 LN:40652 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:3e06b6741061ad93a8587531307057d8
    @SQ SN:chrUn_gl000233 LN:45941 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:7fed60298a8d62ff808b74b6ce820001
    @SQ SN:chrUn_gl000234 LN:40531 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:93f998536b61a56fd0ff47322a911d4b
    @SQ SN:chrUn_gl000235 LN:34474 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:118a25ca210cfbcdfb6c2ebb249f9680
    @SQ SN:chrUn_gl000236 LN:41934 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:fdcd739913efa1fdc64b6c0cd7016779
    @SQ SN:chrUn_gl000237 LN:45867 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:e0c82e7751df73f4f6d0ed30cdc853c0
    @SQ SN:chrUn_gl000238 LN:39939 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:131b1efc3270cc838686b54e7c34b17b
    @SQ SN:chrUn_gl000239 LN:33824 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:99795f15702caec4fa1c4e15f8a29c07
    @SQ SN:chrUn_gl000240 LN:41933 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:445a86173da9f237d7bcf41c6cb8cc62
    @SQ SN:chrUn_gl000241 LN:42152 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:ef4258cdc5a45c206cea8fc3e1d858cf
    @SQ SN:chrUn_gl000242 LN:43523 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:2f8694fc47576bc81b5fe9e7de0ba49e
    @SQ SN:chrUn_gl000243 LN:43341 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:cc34279a7e353136741c9fce79bc4396
    @SQ SN:chrUn_gl000244 LN:39929 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:0996b4475f353ca98bacb756ac479140
    @SQ SN:chrUn_gl000245 LN:36651 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:89bc61960f37d94abf0df2d481ada0ec
    @SQ SN:chrUn_gl000246 LN:38154 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:e4afcd31912af9d9c2546acf1cb23af2
    @SQ SN:chrUn_gl000247 LN:36422 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:7de00226bb7df1c57276ca6baabafd15
    @SQ SN:chrUn_gl000248 LN:39786 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:5a8e43bec9be36c7b49c84d585107776
    @SQ SN:chrUn_gl000249 LN:38502 UR:file:/humgen/gsa-hpprojects/GATK/bundle/ucsc.hg19/ucsc.hg19.fasta M5:1d78abec37c15fe29a275eb08d5af236
    @RG ID:id PL:platform PU:machine LB:library SM:sample
    @PG ID:STAR PN:STAR VN:STAR_2.4.2a CL:STAR-2.4.2a --runThreadN 10 --genomeDir /gcg/husar/gcgdata/ngsdata/STAR/human_genome37 --readFilesIn /ngs/m/L201/Analysis/AML_Stroma_pat_4/Analysis_cutadapt/output/BM_ID_ATCACG_L003_readp_1.fastq.trimmed.fastq.gz /ngs/m/L201/Analysis/AML_Stroma_pat_4/Analysis_cutadapt/output/BM_ID_ATCACG_L003_readp_2.fastq.trimmed.fastq.gz --readFilesCommand zcat --outFileNamePrefix /ngs/m/L201/Analysis/AML_Stroma_pat_4/Star_align/output/BM_ID_ATCACG_L003_readp.txt --outStd SAM --outReadsUnmapped Fastx --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS --outSAMunmapped Within --outSAMattrRGline ID:1 PL:illumina PU:BM_ID_ATCACG_L003_readp SM:AML --outFilterMultimapNmax 10
    @CO user command line:

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Alva
    Hi,

    So, you do not have a dictionary file for your reference? That might be the issue. Have a look at this article for more information: http://gatkforums.broadinstitute.org/discussion/2798/howto-prepare-a-reference-for-use-with-bwa-and-gatk#latest

    -Sheila

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