Entering edit mode
6 months ago
bitpir ▴ 210
I ran freebayes using the following command line:
##freebayes -b <bam> -f hg38.noalt.fa -v <vcf> --min-alternate-count 3 --min-alternate-fraction 0.2 -t b.bed"
One of the samples have this following output:
chr1 179109038 . A C 0.014237 . AB=0.235294;ABP=13.3567;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=11.6962;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.71882;PAIRED=1;PAIREDR=0.846154;PAO=0;PQA=0;PQR=0;PRO=0;QA=108;QR=460;RO=13;RPL=4;RPP=11.6962;RPPR=3.17734;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=31.2394;SRR=13;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:17:13,4:13:460:4:108:-4.86964,0,-36.5987
And the other one has this:
chr1 179109038 . A C 51.8359 . AB=0.448276;ABP=3.68421;AC=1;AF=0.5;AN=2;AO=13;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=31.2394;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=51.4615;MQMR=60;NS=1;NUMALT=1;ODDS=11.9357;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=343;QR=601;RO=16;RPL=13;RPP=31.2394;RPPR=3.55317;RPR=0;RUN=1;SAF=13;SAP=31.2394;SAR=0;SRF=2;SRP=22.5536;SRR=14;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:29:16,13:16:601:13:343:-19.822,0,-45.6764
This variant is a false-positive when compared to NA12878 benchmark.vcf. I am unclear as to how one sample has low QUAL and the other a high QUAL. The BQ and MAPQ for these 2 samples are very similar -- 35 and 57, respectively. Per Freebayes best-practices, I should do vcffilter based on the QUAL, but I would like to understand more what contributes to the QUAL score in this situation?
Any idea would be greatly appreciated! Thanks!
We know that false positive issue happens in variant caling tools. You can read benchmarking papers about this. Nevertheless, I would consider AD and DP field in vcf file as well. Maybe you should filter your vcf using these definitions (DP, MAPQ) instead QUAL.