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HaplotypeCaller error: Badly formed genome unclippedLoc: Query interval is not valid for this input

minimaxminimax Member
edited May 30 in Ask the GATK team

Hi there,

I'm running the GATK best practice pipeline (locally on a Linux server without using docker) for Germline short variant discovery (SNPs + Indels) using the Generic germline short variant per-sample calling on whole exome data.

When I run the haplotypecaller with -L argument, I got the following error:

A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "@HD    VN:1.0  SO:coordinate" is not valid for this input.

It seems that the pipeline could not recognize that the intervals are in Picard-style.

My interval lists are provided by the sequencing provider in an MS excel file (which contains all the intervals), I save it as a "tab delimited text", which is actually space-delimited. So I use sed to make it tab-delimited, and manually change its suffix to .interval_list (since it has a SAM-like header---see below its contents, so I guess it should be in picard-style?), and used this file for the -L argument.

I both googled and searched this forum, but did not find any solution for my problem. I'm new to this area and really appreciate your help! Thank you!!

For your reference, below are the related codes:

${gatk_path}/gatk --java-options "-Xmx39G -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10" \
      HaplotypeCaller \
      -R Homo_sapiens_assembly19.fasta \
      -I my.bam \
      -L TargetList.interval_list \
      -O my.g.vcf.gz \
      -contamination 0 -ERC GVCF

The interval list file TargetList.interval_list (which contains all the intervals) looks like this:

@HD VN:1.0  SO:coordinate
@SQ SN:1    LN:249250621    UR:   AS:GRCh37   M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapiens
@SQ SN:2    LN:243199373    UR:   AS:GRCh37   M5:a0d9851da00400dec1098a9255ac712e SP:Homo Sapiens
@SQ SN:3    LN:198022430    UR:   AS:GRCh37   M5:fdfd811849cc2fadebc929bb925902e5 SP:Homo Sapiens
@SQ SN:4    LN:191154276    UR:   AS:GRCh37   M5:23dccd106897542ad87d2765d28a19a1 SP:Homo Sapiens
@SQ SN:5    LN:180915260    UR:   AS:GRCh37   M5:0740173db9ffd264d728f32784845cd7 SP:Homo Sapiens
@SQ SN:6    LN:171115067    UR:   AS:GRCh37   M5:1d3a93a248d92a729ee764823acbbc6b SP:Homo Sapiens
@SQ SN:7    LN:159138663    UR:   AS:GRCh37   M5:618366e953d6aaad97dbe4777c29375e SP:Homo Sapiens
@SQ SN:8    LN:146364022    UR:   AS:GRCh37   M5:96f514a9929e410c6651697bded59aec SP:Homo Sapiens
@SQ SN:9    LN:141213431    UR:   AS:GRCh37   M5:3e273117f15e0a400f01055d9f393768 SP:Homo Sapiens
@SQ SN:10   LN:135534747    UR:   AS:GRCh37   M5:988c28e000e84c26d552359af1ea2e1d SP:Homo Sapiens
@SQ SN:11   LN:135006516    UR:   AS:GRCh37   M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Homo Sapiens
@SQ SN:12   LN:133851895    UR:   AS:GRCh37   M5:51851ac0e1a115847ad36449b0015864 SP:Homo Sapiens
@SQ SN:13   LN:115169878    UR:   AS:GRCh37   M5:283f8d7892baa81b510a015719ca7b0b SP:Homo Sapiens
@SQ SN:14   LN:107349540    UR:   AS:GRCh37   M5:98f3cae32b2a2e9524bc19813927542e SP:Homo Sapiens
@SQ SN:15   LN:102531392    UR:   AS:GRCh37   M5:e5645a794a8238215b2cd77acb95a078 SP:Homo Sapiens
@SQ SN:16   LN:90354753 UR:   AS:GRCh37   M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Homo Sapiens
@SQ SN:17   LN:81195210 UR:   AS:GRCh37   M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Homo Sapiens
@SQ SN:18   LN:78077248 UR:   AS:GRCh37   M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Homo Sapiens
@SQ SN:19   LN:59128983 UR:   AS:GRCh37   M5:1aacd71f30db8e561810913e0b72636d SP:Homo Sapiens
@SQ SN:20   LN:63025520 UR:   AS:GRCh37   M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo Sapiens
@SQ SN:21   LN:48129895 UR:   AS:GRCh37   M5:2979a6085bfe28e3ad6f552f361ed74d SP:Homo Sapiens
@SQ SN:22   LN:51304566 UR:   AS:GRCh37   M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo Sapiens
@SQ SN:X    LN:155270560    UR:   AS:GRCh37   M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo Sapiens
@SQ SN:Y    LN:59373566 UR:   AS:GRCh37   M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Homo Sapiens
@SQ SN:MT   LN:16569    UR:   AS:GRCh37   M5:c68f52674c9fb33aef52dcf399755519 SP:Homo Sapiens
@SQ SN:GL000207.1   LN:4262 UR:   AS:GRCh37   M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Homo Sapiens
@SQ SN:GL000226.1   LN:15008    UR:   AS:GRCh37   M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Homo Sapiens
@SQ SN:GL000229.1   LN:19913    UR:   AS:GRCh37   M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Homo Sapiens
@SQ SN:GL000231.1   LN:27386    UR:   AS:GRCh37   M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Homo Sapiens
@SQ SN:GL000210.1   LN:27682    UR:   AS:GRCh37   M5:851106a74238044126131ce2a8e5847c SP:Homo Sapiens
@SQ SN:GL000239.1   LN:33824    UR:   AS:GRCh37   M5:99795f15702caec4fa1c4e15f8a29c07 SP:Homo Sapiens
@SQ SN:GL000235.1   LN:34474    UR:   AS:GRCh37   M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Homo Sapiens
@SQ SN:GL000201.1   LN:36148    UR:   AS:GRCh37   M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Homo Sapiens
@SQ SN:GL000247.1   LN:36422    UR:   AS:GRCh37   M5:7de00226bb7df1c57276ca6baabafd15 SP:Homo Sapiens
@SQ SN:GL000245.1   LN:36651    UR:   AS:GRCh37   M5:89bc61960f37d94abf0df2d481ada0ec SP:Homo Sapiens
@SQ SN:GL000197.1   LN:37175    UR:   AS:GRCh37   M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Homo Sapiens
@SQ SN:GL000203.1   LN:37498    UR:   AS:GRCh37   M5:96358c325fe0e70bee73436e8bb14dbd SP:Homo Sapiens
@SQ SN:GL000246.1   LN:38154    UR:   AS:GRCh37   M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Homo Sapiens
@SQ SN:GL000249.1   LN:38502    UR:   AS:GRCh37   M5:1d78abec37c15fe29a275eb08d5af236 SP:Homo Sapiens
@SQ SN:GL000196.1   LN:38914    UR:   AS:GRCh37   M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Homo Sapiens
@SQ SN:GL000248.1   LN:39786    UR:   AS:GRCh37   M5:5a8e43bec9be36c7b49c84d585107776 SP:Homo Sapiens
@SQ SN:GL000244.1   LN:39929    UR:   AS:GRCh37   M5:0996b4475f353ca98bacb756ac479140 SP:Homo Sapiens
@SQ SN:GL000238.1   LN:39939    UR:   AS:GRCh37   M5:131b1efc3270cc838686b54e7c34b17b SP:Homo Sapiens
@SQ SN:GL000202.1   LN:40103    UR:   AS:GRCh37   M5:06cbf126247d89664a4faebad130fe9c SP:Homo Sapiens
@SQ SN:GL000234.1   LN:40531    UR:   AS:GRCh37   M5:93f998536b61a56fd0ff47322a911d4b SP:Homo Sapiens
@SQ SN:GL000232.1   LN:40652    UR:   AS:GRCh37   M5:3e06b6741061ad93a8587531307057d8 SP:Homo Sapiens
@SQ SN:GL000206.1   LN:41001    UR:   AS:GRCh37   M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Homo Sapiens
@SQ SN:GL000240.1   LN:41933    UR:   AS:GRCh37   M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Homo Sapiens
@SQ SN:GL000236.1   LN:41934    UR:   AS:GRCh37   M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Homo Sapiens
@SQ SN:GL000241.1   LN:42152    UR:   AS:GRCh37   M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Homo Sapiens
@SQ SN:GL000243.1   LN:43341    UR:   AS:GRCh37   M5:cc34279a7e353136741c9fce79bc4396 SP:Homo Sapiens
@SQ SN:GL000242.1   LN:43523    UR:   AS:GRCh37   M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Homo Sapiens
@SQ SN:GL000230.1   LN:43691    UR:   AS:GRCh37   M5:b4eb71ee878d3706246b7c1dbef69299 SP:Homo Sapiens
@SQ SN:GL000237.1   LN:45867    UR:   AS:GRCh37   M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Homo Sapiens
@SQ SN:GL000233.1   LN:45941    UR:   AS:GRCh37   M5:7fed60298a8d62ff808b74b6ce820001 SP:Homo Sapiens
@SQ SN:GL000204.1   LN:81310    UR:   AS:GRCh37   M5:efc49c871536fa8d79cb0a06fa739722 SP:Homo Sapiens
@SQ SN:GL000198.1   LN:90085    UR:   AS:GRCh37   M5:868e7784040da90d900d2d1b667a1383 SP:Homo Sapiens
@SQ SN:GL000208.1   LN:92689    UR:   AS:GRCh37   M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Homo Sapiens
@SQ SN:GL000191.1   LN:106433   UR:   AS:GRCh37   M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Homo Sapiens
@SQ SN:GL000227.1   LN:128374   UR:   AS:GRCh37   M5:a4aead23f8053f2655e468bcc6ecdceb SP:Homo Sapiens
@SQ SN:GL000228.1   LN:129120   UR:   AS:GRCh37   M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Homo Sapiens
@SQ SN:GL000214.1   LN:137718   UR:   AS:GRCh37   M5:46c2032c37f2ed899eb41c0473319a69 SP:Homo Sapiens
@SQ SN:GL000221.1   LN:155397   UR:   AS:GRCh37   M5:3238fb74ea87ae857f9c7508d315babb SP:Homo Sapiens
@SQ SN:GL000209.1   LN:159169   UR:   AS:GRCh37   M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Homo Sapiens
@SQ SN:GL000218.1   LN:161147   UR:   AS:GRCh37   M5:1d708b54644c26c7e01c2dad5426d38c SP:Homo Sapiens
@SQ SN:GL000220.1   LN:161802   UR:   AS:GRCh37   M5:fc35de963c57bf7648429e6454f1c9db SP:Homo Sapiens
@SQ SN:GL000213.1   LN:164239   UR:   AS:GRCh37   M5:9d424fdcc98866650b58f004080a992a SP:Homo Sapiens
@SQ SN:GL000211.1   LN:166566   UR:   AS:GRCh37   M5:7daaa45c66b288847b9b32b964e623d3 SP:Homo Sapiens
@SQ SN:GL000199.1   LN:169874   UR:   AS:GRCh37   M5:569af3b73522fab4b40995ae4944e78e SP:Homo Sapiens
@SQ SN:GL000217.1   LN:172149   UR:   AS:GRCh37   M5:6d243e18dea1945fb7f2517615b8f52e SP:Homo Sapiens
@SQ SN:GL000216.1   LN:172294   UR:   AS:GRCh37   M5:642a232d91c486ac339263820aef7fe0 SP:Homo Sapiens
@SQ SN:GL000215.1   LN:172545   UR:   AS:GRCh37   M5:5eb3b418480ae67a997957c909375a73 SP:Homo Sapiens
@SQ SN:GL000205.1   LN:174588   UR:   AS:GRCh37   M5:d22441398d99caf673e9afb9a1908ec5 SP:Homo Sapiens
@SQ SN:GL000219.1   LN:179198   UR:   AS:GRCh37   M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Homo Sapiens
@SQ SN:GL000224.1   LN:179693   UR:   AS:GRCh37   M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Homo Sapiens
@SQ SN:GL000223.1   LN:180455   UR:   AS:GRCh37   M5:399dfa03bf32022ab52a846f7ca35b30 SP:Homo Sapiens
@SQ SN:GL000195.1   LN:182896   UR:   AS:GRCh37   M5:5d9ec007868d517e73543b005ba48535 SP:Homo Sapiens
@SQ SN:GL000212.1   LN:186858   UR:   AS:GRCh37   M5:563531689f3dbd691331fd6c5730a88b SP:Homo Sapiens
@SQ SN:GL000222.1   LN:186861   UR:   AS:GRCh37   M5:6fe9abac455169f50470f5a6b01d0f59 SP:Homo Sapiens
@SQ SN:GL000200.1   LN:187035   UR:   AS:GRCh37   M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Homo Sapiens
@SQ SN:GL000193.1   LN:189789   UR:   AS:GRCh37   M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens
@SQ SN:GL000194.1   LN:191469   UR:   AS:GRCh37   M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens
@SQ SN:GL000225.1   LN:211173   UR:   AS:GRCh37   M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens
@SQ SN:GL000192.1   LN:547496   UR:   AS:GRCh37   M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens
@SQ SN:NC_007605    LN:171823   UR:   AS:NC_007605.1  M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus
@PG ID:1    PN:IntervalListTools    CL:net.sf.picard.util.IntervalListTools INPUT=[Homo_sapiens_assembly19.dict] OUTPUT=targets.interval_list UNIQUE=false SORT=true    PADDING=0 SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
1   12191   12227   +   CEX-chr1-12190-12227
1   12596   12721   +   CEX-chr1-12595-12721


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