search

tamsen / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
7 stars 0 forks source link

VCF file contains all covered positions #12

Closed mkazanov closed 2 years ago

mkazanov commented 2 years ago

Hi Tamsen,

I run the following command: /pisces_all/Pisces -bam /my/my.bam -g /HUMAN/FASTA/ -o /my/out and got a very big VCF file (~10GB) with, I guess, all covered positions (first lines below): Genome directory contains hg19.fa genome file, hg19.fa.fai index file and GenomeSize.xml (full file is below) created using CreateGenomeSizeFile tool. What am I doing wrong?

VCF file:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  427.bam
chr1    10541   .   C   .   37  LowDP   DP=2    GT:GQ:AD:DP:VF:NL:SB    ./.:0:2:2:0.000:20:-20.0643
chr1    10542   .   C   .   37  LowDP   DP=2    GT:GQ:AD:DP:VF:NL:SB    ./.:0:2:2:0.000:20:-20.0643
chr1    10543   .   G   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10544   .   A   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10545   .   A   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10546   .   A   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10547   .   T   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10548   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10549   .   T   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10550   .   G   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10551   .   T   .   37  LowDP   DP=2    GT:GQ:AD:DP:VF:NL:SB    ./.:0:2:2:0.000:20:-20.0643
chr1    10552   .   G   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10553   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10554   .   A   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10555   .   G   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10556   .   A   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10557   .   G   .   37  LowDP   DP=2    GT:GQ:AD:DP:VF:NL:SB    ./.:0:2:2:0.000:20:-20.0643
chr1    10558   .   G   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10559   .   A   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10560   .   C   G   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:0,3:3:1.000:20:-20.0225
chr1    10561   .   A   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10562   .   A   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10563   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10564   .   G   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10565   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10566   .   A   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10567   .   G   .   37  LowDP   DP=2    GT:GQ:AD:DP:VF:NL:SB    ./.:0:2:2:0.000:20:-20.0643
chr1    10568   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10569   .   T   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10570   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10571   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10572   .   G   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10573   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10574   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10575   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10576   .   T   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
chr1    10577   .   C   .   54  LowDP   DP=3    GT:GQ:AD:DP:VF:NL:SB    ./.:0:3:3:0.000:20:-20.0225
....

GenomeSize.xml file:

<?xml version="1.0" encoding="utf-8"?>
<sequenceSizes genomeName="Homo sapiens hg19">
    <chromosome fileName="hg19.fa" contigName="chr1" totalBases="249250621" isCircular="false" md5="1b22b98cdeb4a9304cb5d48026a85128" ploidy="2" knownBases="225280621" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr2" totalBases="243199373" isCircular="false" md5="a0d9851da00400dec1098a9255ac712e" ploidy="2" knownBases="238204518" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr3" totalBases="198022430" isCircular="false" md5="641e4338fa8d52a5b781bd2a2c08d3c3" ploidy="2" knownBases="194797135" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr4" totalBases="191154276" isCircular="false" md5="23dccd106897542ad87d2765d28a19a1" ploidy="2" knownBases="187661676" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr5" totalBases="180915260" isCircular="false" md5="0740173db9ffd264d728f32784845cd7" ploidy="2" knownBases="177695260" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr6" totalBases="171115067" isCircular="false" md5="1d3a93a248d92a729ee764823acbbc6b" ploidy="2" knownBases="167395066" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr7" totalBases="159138663" isCircular="false" md5="618366e953d6aaad97dbe4777c29375e" ploidy="2" knownBases="155353663" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrX" totalBases="155270560" isCircular="false" md5="7e0e2e580297b7764e31dbc80c2540dd" ploidy="2" knownBases="151100560" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr8" totalBases="146364022" isCircular="false" md5="96f514a9929e410c6651697bded59aec" ploidy="2" knownBases="142888922" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr9" totalBases="141213431" isCircular="false" md5="3e273117f15e0a400f01055d9f393768" ploidy="2" knownBases="120143431" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr10" totalBases="135534747" isCircular="false" md5="988c28e000e84c26d552359af1ea2e1d" ploidy="2" knownBases="131314738" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr11" totalBases="135006516" isCircular="false" md5="98c59049a2df285c76ffb1c6db8f8b96" ploidy="2" knownBases="131129516" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr12" totalBases="133851895" isCircular="false" md5="51851ac0e1a115847ad36449b0015864" ploidy="2" knownBases="130481393" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr13" totalBases="115169878" isCircular="false" md5="283f8d7892baa81b510a015719ca7b0b" ploidy="2" knownBases="95589878" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr14" totalBases="107349540" isCircular="false" md5="98f3cae32b2a2e9524bc19813927542e" ploidy="2" knownBases="88289540" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr15" totalBases="102531392" isCircular="false" md5="e5645a794a8238215b2cd77acb95a078" ploidy="2" knownBases="81694766" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr16" totalBases="90354753" isCircular="false" md5="fc9b1a7b42b97a864f56b348b06095e6" ploidy="2" knownBases="78884753" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr17" totalBases="81195210" isCircular="false" md5="351f64d4f4f9ddd45b35336ad97aa6de" ploidy="2" knownBases="77795210" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr18" totalBases="78077248" isCircular="false" md5="b15d4b2d29dde9d3e4f93d1d0f2cbc9c" ploidy="2" knownBases="74657229" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr20" totalBases="63025520" isCircular="false" md5="0dec9660ec1efaaf33281c0d5ea2560f" ploidy="2" knownBases="59505520" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrY" totalBases="59373566" isCircular="false" md5="1e86411d73e6f00a10590f976be01623" ploidy="2" knownBases="25653566" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr19" totalBases="59128983" isCircular="false" md5="1aacd71f30db8e561810913e0b72636d" ploidy="2" knownBases="55808983" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr22" totalBases="51304566" isCircular="false" md5="a718acaa6135fdca8357d5bfe94211dd" ploidy="2" knownBases="34894545" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr21" totalBases="48129895" isCircular="false" md5="2979a6085bfe28e3ad6f552f361ed74d" ploidy="2" knownBases="35106642" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr6_ssto_hap7" totalBases="4928567" isCircular="false" md5="3b6d666200e72bcc036bf88a4d7e0749" ploidy="2" knownBases="4173551" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr6_mcf_hap5" totalBases="4833398" isCircular="false" md5="efed415dd8742349cb7aaca054675b9a" ploidy="2" knownBases="3794911" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr6_cox_hap2" totalBases="4795371" isCircular="false" md5="18c17e1641ef04873b15f40f6c8659a4" ploidy="2" knownBases="4795371" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr6_mann_hap4" totalBases="4683263" isCircular="false" md5="9d51d4152174461cd6715c7ddc588dc8" ploidy="2" knownBases="4100741" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr6_apd_hap1" totalBases="4622290" isCircular="false" md5="fe71bc63420d666884f37a3ad79f3317" ploidy="2" knownBases="2320747" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr6_qbl_hap6" totalBases="4611984" isCircular="false" md5="094d037050cad692b57ea12c4fef790f" ploidy="2" knownBases="4295325" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr6_dbb_hap3" totalBases="4610396" isCircular="false" md5="2a3c677c426a10e137883ae1ffb8da3f" ploidy="2" knownBases="4204302" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr17_ctg5_hap1" totalBases="1680828" isCircular="false" md5="d89517b400226d3b56e753972a7cad67" ploidy="2" knownBases="1580828" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr4_ctg9_hap1" totalBases="590426" isCircular="false" md5="fa24f81b680df26bcfb6d69b784fbe36" ploidy="2" knownBases="590426" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr1_gl000192_random" totalBases="547496" isCircular="false" md5="325ba9e808f669dfeee210fdd7b470ac" ploidy="2" knownBases="547496" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000225" totalBases="211173" isCircular="false" md5="63945c3e6962f28ffd469719a747e73c" ploidy="2" knownBases="211173" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr4_gl000194_random" totalBases="191469" isCircular="false" md5="6ac8f815bf8e845bb3031b73f812c012" ploidy="2" knownBases="191469" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr4_gl000193_random" totalBases="189789" isCircular="false" md5="dbb6e8ece0b5de29da56601613007c2a" ploidy="2" knownBases="189789" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr9_gl000200_random" totalBases="187035" isCircular="false" md5="75e4c8d17cd4addf3917d1703cacaf25" ploidy="2" knownBases="187035" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000222" totalBases="186861" isCircular="false" md5="6fe9abac455169f50470f5a6b01d0f59" ploidy="2" knownBases="186861" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000212" totalBases="186858" isCircular="false" md5="563531689f3dbd691331fd6c5730a88b" ploidy="2" knownBases="186858" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr7_gl000195_random" totalBases="182896" isCircular="false" md5="5d9ec007868d517e73543b005ba48535" ploidy="2" knownBases="182896" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000223" totalBases="180455" isCircular="false" md5="399dfa03bf32022ab52a846f7ca35b30" ploidy="2" knownBases="180455" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000224" totalBases="179693" isCircular="false" md5="d5b2fc04f6b41b212a4198a07f450e20" ploidy="2" knownBases="179693" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000219" totalBases="179198" isCircular="false" md5="f977edd13bac459cb2ed4a5457dba1b3" ploidy="2" knownBases="179198" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr17_gl000205_random" totalBases="174588" isCircular="false" md5="d22441398d99caf673e9afb9a1908ec5" ploidy="2" knownBases="174588" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000215" totalBases="172545" isCircular="false" md5="5eb3b418480ae67a997957c909375a73" ploidy="2" knownBases="172545" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000216" totalBases="172294" isCircular="false" md5="642a232d91c486ac339263820aef7fe0" ploidy="2" knownBases="172294" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000217" totalBases="172149" isCircular="false" md5="6d243e18dea1945fb7f2517615b8f52e" ploidy="2" knownBases="172149" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr9_gl000199_random" totalBases="169874" isCircular="false" md5="569af3b73522fab4b40995ae4944e78e" ploidy="2" knownBases="169874" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000211" totalBases="166566" isCircular="false" md5="7daaa45c66b288847b9b32b964e623d3" ploidy="2" knownBases="166566" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000213" totalBases="164239" isCircular="false" md5="9d424fdcc98866650b58f004080a992a" ploidy="2" knownBases="164239" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000220" totalBases="161802" isCircular="false" md5="fc35de963c57bf7648429e6454f1c9db" ploidy="2" knownBases="161802" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000218" totalBases="161147" isCircular="false" md5="1d708b54644c26c7e01c2dad5426d38c" ploidy="2" knownBases="161147" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr19_gl000209_random" totalBases="159169" isCircular="false" md5="f40598e2a5a6b26e84a3775e0d1e2c81" ploidy="2" knownBases="159169" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000221" totalBases="155397" isCircular="false" md5="3238fb74ea87ae857f9c7508d315babb" ploidy="2" knownBases="155397" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000214" totalBases="137718" isCircular="false" md5="46c2032c37f2ed899eb41c0473319a69" ploidy="2" knownBases="137718" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000228" totalBases="129120" isCircular="false" md5="c5a17c97e2c1a0b6a9cc5a6b064b714f" ploidy="2" knownBases="129120" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000227" totalBases="128374" isCircular="false" md5="a4aead23f8053f2655e468bcc6ecdceb" ploidy="2" knownBases="128374" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr1_gl000191_random" totalBases="106433" isCircular="false" md5="d75b436f50a8214ee9c2a51d30b2c2cc" ploidy="2" knownBases="106433" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr19_gl000208_random" totalBases="92689" isCircular="false" md5="aa81be49bf3fe63a79bdc6a6f279abf6" ploidy="2" knownBases="92689" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr9_gl000198_random" totalBases="90085" isCircular="false" md5="868e7784040da90d900d2d1b667a1383" ploidy="2" knownBases="90085" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr17_gl000204_random" totalBases="81310" isCircular="false" md5="efc49c871536fa8d79cb0a06fa739722" ploidy="2" knownBases="81310" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000233" totalBases="45941" isCircular="false" md5="7fed60298a8d62ff808b74b6ce820001" ploidy="2" knownBases="45941" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000237" totalBases="45867" isCircular="false" md5="e0c82e7751df73f4f6d0ed30cdc853c0" ploidy="2" knownBases="45867" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000230" totalBases="43691" isCircular="false" md5="b4eb71ee878d3706246b7c1dbef69299" ploidy="2" knownBases="43691" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000242" totalBases="43523" isCircular="false" md5="2f8694fc47576bc81b5fe9e7de0ba49e" ploidy="2" knownBases="43523" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000243" totalBases="43341" isCircular="false" md5="cc34279a7e353136741c9fce79bc4396" ploidy="2" knownBases="43341" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000241" totalBases="42152" isCircular="false" md5="ef4258cdc5a45c206cea8fc3e1d858cf" ploidy="2" knownBases="42152" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000236" totalBases="41934" isCircular="false" md5="fdcd739913efa1fdc64b6c0cd7016779" ploidy="2" knownBases="41934" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000240" totalBases="41933" isCircular="false" md5="445a86173da9f237d7bcf41c6cb8cc62" ploidy="2" knownBases="41933" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr17_gl000206_random" totalBases="41001" isCircular="false" md5="43f69e423533e948bfae5ce1d45bd3f1" ploidy="2" knownBases="41001" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000232" totalBases="40652" isCircular="false" md5="3e06b6741061ad93a8587531307057d8" ploidy="2" knownBases="40652" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000234" totalBases="40531" isCircular="false" md5="93f998536b61a56fd0ff47322a911d4b" ploidy="2" knownBases="40531" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr11_gl000202_random" totalBases="40103" isCircular="false" md5="06cbf126247d89664a4faebad130fe9c" ploidy="2" knownBases="40103" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000238" totalBases="39939" isCircular="false" md5="131b1efc3270cc838686b54e7c34b17b" ploidy="2" knownBases="39939" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000244" totalBases="39929" isCircular="false" md5="0996b4475f353ca98bacb756ac479140" ploidy="2" knownBases="39929" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000248" totalBases="39786" isCircular="false" md5="5a8e43bec9be36c7b49c84d585107776" ploidy="2" knownBases="39786" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr8_gl000196_random" totalBases="38914" isCircular="false" md5="d92206d1bb4c3b4019c43c0875c06dc0" ploidy="2" knownBases="38914" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000249" totalBases="38502" isCircular="false" md5="1d78abec37c15fe29a275eb08d5af236" ploidy="2" knownBases="38502" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000246" totalBases="38154" isCircular="false" md5="e4afcd31912af9d9c2546acf1cb23af2" ploidy="2" knownBases="38154" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr17_gl000203_random" totalBases="37498" isCircular="false" md5="96358c325fe0e70bee73436e8bb14dbd" ploidy="2" knownBases="37498" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr8_gl000197_random" totalBases="37175" isCircular="false" md5="6f5efdd36643a9b8c8ccad6f2f1edc7b" ploidy="2" knownBases="37075" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000245" totalBases="36651" isCircular="false" md5="89bc61960f37d94abf0df2d481ada0ec" ploidy="2" knownBases="36651" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000247" totalBases="36422" isCircular="false" md5="7de00226bb7df1c57276ca6baabafd15" ploidy="2" knownBases="36422" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr9_gl000201_random" totalBases="36148" isCircular="false" md5="dfb7e7ec60ffdcb85cb359ea28454ee9" ploidy="2" knownBases="36148" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000235" totalBases="34474" isCircular="false" md5="118a25ca210cfbcdfb6c2ebb249f9680" ploidy="2" knownBases="34474" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000239" totalBases="33824" isCircular="false" md5="99795f15702caec4fa1c4e15f8a29c07" ploidy="2" knownBases="33824" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr21_gl000210_random" totalBases="27682" isCircular="false" md5="851106a74238044126131ce2a8e5847c" ploidy="2" knownBases="27582" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000231" totalBases="27386" isCircular="false" md5="ba8882ce3a1efa2080e5d29b956568a4" ploidy="2" knownBases="27386" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000229" totalBases="19913" isCircular="false" md5="d0f40ec87de311d8e715b52e4c7062e1" ploidy="2" knownBases="19913" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrM" totalBases="16571" isCircular="false" md5="d2ed829b8a1628d16cbeee88e88e39eb" ploidy="2" knownBases="16571" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chrUn_gl000226" totalBases="15008" isCircular="false" md5="1c1b2cd1fccbc0a99b6a447fa24d1504" ploidy="2" knownBases="15008" type="Unknown" />
    <chromosome fileName="hg19.fa" contigName="chr18_gl000207_random" totalBases="4262" isCircular="false" md5="f3814841f1939d3ca19072d9e89f3fd7" ploidy="2" knownBases="4262" type="Unknown" />
</sequenceSizes>
tamsen commented 2 years ago

Hi there,

Thanks for your interest. So is your issue that you do not want all the positions output to vcf? Adding "-gVCF false" to your command line cause the application to just emit called variants. You can run "pisces -h" to get a full list of input options.

Here's an example command line I used recently,

Pisces_cmdline=""-bam /rhome/tdunn011/bigdata/FragariaVescaSubspBracteata/SRR10581356/SRR10581356.trimmed.chrfiltered.rg.Fvb0.marked_duplicates.bam -CallMNVs false -g /rhome/tdunn011/bigdata/Genomes/FragariaVesca/subspBracteata/Fvb2014 -gVCF false -OutFolder /rhome/tdunn011/bigdata/FragariaVescaSubspBracteata/SRR10581356 -FilterDuplicates true -EnableSingleStrandFilter true -MaxVQ 100000""

and it only reported variants, not reference calls.

best Tamsen

mkazanov commented 2 years ago

Thank you for your answer!