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Is this a bug? #508

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zhangrengang opened this issue Nov 20, 2018 · 3 comments
Closed

Is this a bug? #508

zhangrengang opened this issue Nov 20, 2018 · 3 comments
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@zhangrengang
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zhangrengang commented Nov 20, 2018 •
edited

This is one record by freebyes. The REF (19) has more reads covered than ALT (2), but the GT is 1/1.

chr01   23785   .       TAAACCCTAAACCC  AAAACCCTAAACCC  236.163 .       AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X13M;DP=33;DPB=45.7143;DPRA=0;EPP=3.0103;EPPR=3.12459;GTI=0;LEN=1;MEANALT=5;MQM=22;MQMR=38.3158;NS=1;NUMALT=1;ODDS=54.3784;PAIRED=1;PAIREDR=1;PAO=4.33333;PQA=84.5;PQR=281.783;PRO=7.81667;QA=44;QR=706;RO=19;RPL=2;RPP=7.35324;RPPR=22.325;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=8;SRP=4.03889;SRR=11;TYPE=snp  GT:DP:AD:RO:QR:AO:QA:GL 1/1:33:19,2:19:706:2:44:-20.492,-56.9638,0

I find another uncorrect call:

$ less freebayes.filter.vcf | grep -P "chr10\t22690856"
chr10   22690856        .       NNNNNNNNNNNNNNNNNNNNN   CCTTTATTGATCGCACTAGCT   64.9393 .       AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=21X;DP=2;DPB=2;DPRA=0;EPP=0;EPPR=0;GTI=0;LEN=21;MEANALT=1;MQM=50.5;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=0;RO=0;RPL=2;RPP=7.35324;RPPR=0;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=complex;technology.illumina=1   GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:82:-7.69777,-0.60206,0

$ samtools tview mapped.bam.rg.bam -p chr10:22690835 --reference ref.fa
      22690841  22690851  22690861  22690871  22690881  22690891  22690901
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                     CCTTTATTGATCGCACTAGCT
                     CCTTTATTGATCGCACTAGCT
                     cctttattgatcgcactagct
$ samtools view mapped.bam.rg.bam chr10:22690856 |less
E00500:171:HHYL3CCXY:1:2219:3934:66918  99      chr10   22690856        49      95S21M35S       =       22690856        21      AGAACTTGCCCGCTTTGTGAGCTTTCGTAAAGTCTAGATCATCCACATCCAATGGTGAGCTACCACCTTGAGCCGGACTAGCGACCATACAAATCCCTTTATTGATCGCACTAGCTTCCGTCAAAAGATAAGCCAAACCAAATCGAGAAAG AAFFFJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ XA:Z:chr12,+27251816,87S19M45S,0;       MC:Z:5S21M124S  MD:Z:21 RG:Z:SR NM:i:0  AS:i:21 XS:i:19
E00500:171:HHYL3CCXY:1:2219:3934:66918  147     chr10   22690856        52      5S21M124S       =       22690856        -21     AAATCCCTTTATTGATCGCACTAGCTTCCGTCAAAAGATAAGCCAAACCAAATCGAGAAAGACATTGTACTGCAAACCCACCTTCTACTGGCACAGAAGAGTCCGCAGGAGGCTTCAACTTTCCAGTAGGTGGTCCACCTTGAGTTTGAA  FAFFJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJFJJJFJFJJAFFJJJJJJ<JJAJJJJJJJJJJJJJJJJJ<JJJFJJJJAJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJFFFA  MC:Z:95S21M35S  MD:Z:21 RG:Z:SR NM:i:0  AS:i:21 XS:i:0

$ less freebayes.filter.vcf | grep -P "chr10\t22691043"
chr10   22691043        .       N       A       62.4838 .       AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=59;MQMR=0;NS=1;NUMALT=1;ODDS=8.76405;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=96;QR=0;RO=0;RPL=0;RPP=9.52472;RPPR=0;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1    GT:DP:AD:RO:QR:AO:QA:GL 1/1:3:0,3:0:0:3:96:-8.95758,-0.90309,0

$ samtools tview mapped.bam.rg.bam -p chr10:22691030 --reference ref.fa
22691031  22691041  22691051  22691061  22691071  22691081  22691091
nnnnnnnnnnnnnntgtgtgcggctaacccttgtaactgagcagttaactgagcaatatgatcagcttgggcctgatgct
             A..................................................................
             A..................................................................
             A..................................................................
             A..................................................................
              ..................................................................
              ..................................................................
              ..................................................................
              ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
$ samtools view mapped.bam.rg.bam chr10:22691030 |less
E00500:171:HHYL3CCXY:1:2117:27255:51096 163     chr10   22691043        59      151M    =       22691098        206     ATGTGTGCGGCTAACCCTTGTAACTGAGCAGTTAACTGAGCAATATGATCAGCTTGGGCCTGATGCTCCCCCTGGCCCTCTGCAGCAGGTGCAGGCTGTTCCTCTGGAGGAGCAGCAGCAAGAGGCACATGAAGAAGATGTGCAGAAGATT AAFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ XA:Z:chr08,-14289051,151M,2;    MC:Z:151M       MD:Z:0C150      RG:Z:SR NM:i:1  AS:i:150        XS:i:141
E00500:171:HHYL3CCXY:1:2117:26890:51658 163     chr10   22691043        59      151M    =       22691098        206     ATGTGTGCGGCTAACCCTTGTAACTGAGCAGTTAACTGAGCAATATGATCAGCTTGGGCCTGATGCTCCCCCTGGCCCTCTGCAGCAGGTGCAGGCTGTTCCTCTGGAGGAGCAGCAGCAAGAGGCACATGAAGAAGATGTGCAGAAGATT AAFAFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJJJJJJJJJJFJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJAJJ XA:Z:chr08,-14289051,151M,2;    MC:Z:151M       MD:Z:0C150      RG:Z:SR NM:i:1  AS:i:150        XS:i:141
E00500:171:HHYL3CCXY:1:2117:26474:51992 163     chr10   22691043        59      151M    =       22691098        206     ATGTGTGCGGCTAACCCTTGTAACTGAGCAGTTAACTGAGCAATATGATCAGCTTGGGCCTGATGCTCCCCCTGGCCCTCTGCAGCAGGTGCAGGCTGTTCCTCTGGAGGAGCAGCAGCAAGAGGCACATGAAGAAGATGTGCAGAAGATT AAFFFJFJJAJ-FJJJFJJJJJJJFJJJFF<JJ-JJJJFJJFFF<JJJJJJJJFJFJ-<JAA<FJJFJJJJJJJJFJJ<JJFJFJJFJFJF<7FJJJJJ<AJA<<FFAFJFFJJJJJJAJFJJJJJ<A-7AFJJFFJFJJJJJAFF7FFFA XA:Z:chr08,-14289051,151M,2;    MC:Z:151M       MD:Z:0C150      RG:Z:SR NM:i:1  AS:i:150        XS:i:141

It seems that the mapper, bwa-mem (v0.7.17), uncorrectly aligned some reads to a gap, and freebayes (v1.2.0) treated it as a variant.
@janxkoci
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janxkoci commented Dec 3, 2018

I don't know the answer, however I know that freebayes does some realingning by himself, maybe that's the discrepancy. Also notice that in the first example the total DP is 33 while if you sum AD you get 21 - some callers do this due to reads' qualities, not sure if it's the case here..

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This issue is marked stale because it has been open 120 days with no activity. Remove stale label or comment or this will be closed in 5 days

@github-actions github-actions bot added the Stale label Dec 11, 2020
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This issue was closed for lack of activity. Feel free to re-open if someone feels like working on it.

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