bcftools not filtering snps

Question

[analyst]

Dear all,

I have called variants through freebayes.

Now I am filtering SNPs and Indels.

Opening SNPs file I found other variants also.

I used this command to filter snps:

bcftools view -v snps -Ov -o snps_only.vcf variants.vcf.gz

Why bcftools not giving desired output please guide to get only snps.

Thank you

[Pierre Lindenbaum]

Why bcftools not giving desired output

show us an example of "not desired output" please

[analyst]

Here you can see there are other variants too other than SNP

NC_068556.1 17730596 SNC_068556.1_17730596 TCC CTC . PASS AB=0.4,0.189189,0.25,0.214286;ABP=5.18177,34.0565,16.0391,12.937;AC=64,2,7,1;AF=0.5,0.5,0.5,0.5;AN=126;AO=10,7,6,3;CIGAR=1X2M,1X1M1X,2X1M,2M1X;DP=925;DPB=24.3333;DPRA=0,0,0,0;EPP=3.0103,3.32051,4.45795,9.52472;EPPR=3.73412;GTI=0;LEN=1,3,2,1;MEANALT=2,5,2,3;MQM=34.4,24.5714,32,29;MQMR=10.6667;NS=1;NUMALT=1;ODDS=13.5723;PAIRED=0.8,0.571429,0.166667,0.666667;PAIREDR=0;PAO=0,1,0,0;PQA=0,34,0,0;PQR=0;PRO=0;QA=261,232,201,104;QR=102;RO=3;RPL=4,3,4,1;RPP=3.87889,3.32051,4.45795,3.73412;RPPR=3.73412;RPR=6,4,2,2;RUN=1,1,1,1;SAF=7,3,4,1;SAP=6.48466,3.32051,4.45795,3.73412;SAR=3,4,2,2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp,complex,mnp,snp;technology.ILLUMINA=1,1,1,1 GT 0/0 0/0 0/0 0/0 ./. 0/0 1/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/0 0/0 0/0 1/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0

NC_068556.1 17731698 SNC_068556.1_17731698 AG GA . PASS AB=0.315789,0.647059,0.277778;ABP=8.61041,6.20364,10.7311;AC=5,46,3;AF=0.5,0.5,0.5;AN=94;AO=6,11,5;CIGAR=2X2M,1X,1X;DP=507;DPB=14;DPRA=0,0,0;EPP=4.45795,4.78696,13.8677;EPPR=0;GTI=0;LEN=2,1,1;MEANALT=3,2,3;MQM=29.3333,59.7273,34.4;MQMR=0;NS=1;NUMALT=1;ODDS=6.22329;PAIRED=1,1,1;PAIREDR=0;PAO=0,0,0;PQA=0,0,0;PQR=0;PRO=0;QA=177,367,150;QR=0;RO=0;RPL=4,10,5;RPP=4.45795,19.0002,13.8677;RPPR=0;RPR=2,1,0;RUN=1,1,1;SAF=6,5,0;SAP=16.0391,3.20771,13.8677;SAR=0,6,5;SRF=0;SRP=0;SRR=0;TYPE=mnp,snp,snp;technology.ILLUMINA=1,1,1 GT ./. 1/1 0/0 ./. 0/0 ./. ./. ./. ./. ./. 0/0 0/0 ./. ./. ./. 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 1/0 0/0 0/0 0/0 ./. 0/0 ./.

NC_068556.1 17731798 SNC_068556.1_17731798 TG AT . PASS AB=0.769231,0.3,0.230769;ABP=11.1951,16.9077,11.1951;AC=47,6,14;AF=0.5,0.5,0.5;AN=84;AO=10,12,3;CIGAR=1X4M,1X,2X;DP=467;DPB=15;DPRA=0,0,0;EPP=3.87889,3.73412,3.73412;EPPR=0;GTI=0;LEN=1,1,2;MEANALT=2,4,2;MQM=46.9,45.6667,52.6667;MQMR=0;NS=1;NUMALT=1;ODDS=1.57526;PAIRED=1,0.833333,1;PAIREDR=0;PAO=0,0,0;PQA=0,0,0;PQR=0;PRO=0;QA=313,371,102;QR=0;RO=0;RPL=3,6,2;RPP=6.48466,3.0103,3.73412;RPPR=0;RPR=7,6,1;RUN=1,1,1;SAF=5,5,1;SAP=3.0103,3.73412,3.73412;SAR=5,7,2;SRF=0;SRP=0;SRR=0;TYPE=snp,snp,complex;technology.ILLUMINA=1,1,1 GT 0/0 ./. 0/0 ./. ./. ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 1/0 ./. ./. ./. 0/0 0/0 1/0 0/0 ./. 1/0 ./. ./. ./. ./. ./. 1/0 1/0 ./. 0/0 0/1 0/0 1/0 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/1 1/0 0/0 1/0 0/0 ./. 0/0 1/0 1/0 0/0 0/0 1/0 ./. 1/0 ./.

NC_068556.1 17813336 SNC_068556.1_17813336 CGTACG CATACG . PASS AB=0.333333,0.357143,0.44,0.333333;ABP=7.35324,5.49198,3.79203,5.9056;AC=35,4,2,1;AF=0.5,0.5,0.5,0.5;AN=78;AO=6,5,11,4;CIGAR=1X,1M1X3M,4M1X1M,1X2M1X1M1X;DP=313;DPB=18;DPRA=0,0,0,0;EPP=4.45795,3.44459,7.94546,3.0103;EPPR=3.73412;GTI=0;LEN=1,1,1,6;MEANALT=1,3,4,3;MQM=60,60,60,59.5;MQMR=60;NS=1;NUMALT=1;ODDS=20.7058;PAIRED=1,0.8,1,0.25;PAIREDR=1;PAO=0,0,0,0;PQA=0,0,0,0;PQR=0;PRO=0;QA=204,171,378,131;QR=401;RO=12;RPL=2,4,5,3;RPP=4.45795,6.91895,3.20771,5.18177;RPPR=3.73412;RPR=4,1,6,1;RUN=1,1,1,1;SAF=2,2,6,1;SAP=4.45795,3.44459,3.20771,5.18177;SAR=4,3,5,3;SRF=6;SRP=3.0103;SRR=6;TYPE=snp,snp,snp,complex;technology.ILLUMINA=1,1,1,1 GT 0/0 0/0 0/0 0/0 0/0 1/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 ./. ./. ./. ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. ./. ./. ./. ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/1 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. ./. ./. ./. ./. 0/0 ./. ./.

Answer 1

[Pierre Lindenbaum]

ah yes, you're right. I don't understand the reason bcftools treat this as "SNP". May be you could ask the question in https://github.com/samtools/htslib/issues .

you want:

 bcftools view -i 'strlen(ALT)==1 && strlen(REF)==1'   -Ov -o snps_only.vcf variants.vcf.gz

[analyst]

Yes exactly thanks Pierre!