BCFToolsMergeBest

Last commit

Scan a VCF file generated by 'bcftools merge --force-samples', identify duplicate samples, keep the best

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar bcftoolsmergebest  [options] Files

Usage: bcftoolsmergebest [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    --rename-samples
      TSV file for manually assigning samples . Syntax: old-name(tab)new-name. 
      Both names must be present in the VCF file
    --version
      print version and exit
    -c
      comma separated list of criteria used to compare to genotype: GQ:best 
      GQ, DP: highest depth, AD : best AD ratio according to diploy genotype, 
      PL: highest value, GQ: better called than no-call, FT: PASS variant are 
      better, RND: random
      Default: GQ,DP,AD,PL,FT,RND

Keywords

merge
vcf
bcftools

Creation Date

20240604

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bcftoolsmergebest/BCFToolsMergeBest.java

Contribute

Issue Tracker: http://github.com/lindenb/jvarkit/issues
Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite bcftoolsmergebest ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Motivation

can a VCF file generated by 'bcftools merge --force-samples', identify duplicate samples, keep the best"

Example

$ bcftools merge --force-samples src/test/resources/rotavirus_rf.vcf.gz src/test/resources/rotavirus_rf.freebayes.vcf.gz  |\
    grep "#CHROM" -A 3
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S1  S2  S3  S4  S5  2:S5    2:S2    2:S4    2:S3    2:S1
RF01    243 .   A   C   0   .   DPB=28;EPPR=3.37221;GTI=0;MQMR=60;NS=5;NUMALT=1;ODDS=7.64661;PAIREDR=1;PQR=0;PRO=0;QR=408;RO=24;RPPR=3.37221;SRF=24;SRP=55.1256;SRR=0;DP=28;AB=0.5;ABP=3.0103;AF=0.1;AO=4;CIGAR=1X;DPRA=1.66667;EPP=11.6962;LEN=1;MEANALT=1;MQM=60;PAIRED=1;PAO=0;PQA=0;QA=68;RPL=4;RPP=11.6962;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;TYPE=snp;AN=10;AC=1 GT:AD:AO:DP:PL:QA:QR:RO ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   0/0:4,0:0:4:0,12,63:0:68:4  0/0:7,1:1:8:0,7,92:17:119:7 0/1:2,2:2:4:20,0,20:34:34:2 0/0:7,1:1:8:0,7,92:17:119:7 0/0:4,0:0:4:0,12,63:0:68:4
RF01    280 .   A   C   0   .   DPB=24;EPPR=4.58955;GTI=0;MQMR=60;NS=5;NUMALT=1;ODDS=6.90616;PAIREDR=1;PQR=0;PRO=0;QR=374;RO=22;RPPR=4.58955;SRF=22;SRP=50.7827;SRR=0;DP=24;AB=0.4;ABP=3.44459;AF=0.1;AO=2;CIGAR=1X;DPRA=1.05263;EPP=3.0103;LEN=1;MEANALT=1;MQM=60;PAIRED=1;PAO=0;PQA=0;QA=34;RPL=1;RPP=3.0103;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;TYPE=snp;AN=10;AC=1  GT:AD:AO:DP:PL:QA:QR:RO ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   0/1:3,2:2:5:17,0,33:34:51:3 0/0:7,0:0:7:0,21,109:0:119:7    0/0:2,0:0:2:0,6,32:0:34:2   0/0:7,0:0:7:0,21,109:0:119:7    0/0:3,0:0:3:0,9,48:0:51:3
RF01    351 .   T   A   0   .   DPB=25;EPPR=3.94093;GTI=1;MQMR=60;NS=5;NUMALT=1;ODDS=8.27411;PAIREDR=1;PQR=0;PRO=0;QR=357;RO=21;RPPR=3.94093;SRF=21;SRP=48.6112;SRR=0;DP=25;AB=0.4;ABP=3.87889;AF=0.2;AO=4;CIGAR=1X;DPRA=1;EPP=11.6962;LEN=1;MEANALT=1;MQM=60;PAIRED=1;PAO=0;PQA=0;QA=68;RPL=0;RPP=11.6962;RPR=4;RUN=1;SAF=4;SAP=11.6962;SAR=0;TYPE=snp;AN=10;AC=2  GT:AD:AO:DP:PL:QA:QR:RO ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   ./.:.:.:.:.:.:.:.   0/0:7,0:0:7:0,21,109:0:119:7    0/1:3,2:2:5:17,0,33:34:51:3 0/0:4,0:0:4:0,12,63:0:68:4  0/1:3,2:2:5:17,0,33:34:51:3 0/0:4,0:0:4:0,12,63:0:68:4


$ bcftools merge --force-samples src/test/resources/rotavirus_rf.vcf.gz src/test/resources/rotavirus_rf.freebayes.vcf.gz  |\
    java -jar dist/jvarkit.jar bcftoolsmergebest |\
    grep "#CHROM" -A 3
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S3  S4  S5  S1  S2
RF01    243 .   A   C   0   .   AB=0.5;ABP=3.0103;AC=1;AF=0.1;AN=10;AO=4;CIGAR=1X;DP=28;DPB=28;DPRA=1.66667;EPP=11.6962;EPPR=3.37221;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=5;NUMALT=1;ODDS=7.64661;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=408;RO=24;RPL=4;RPP=11.6962;RPPR=3.37221;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=24;SRP=55.1256;SRR=0;TYPE=snp GT:AD:AO:DP:PL:QA:QR:RO 0/0:7,1:1:8:0,7,92:17:119:7 0/1:2,2:2:4:20,0,20:34:34:2 0/0:4,0:0:4:0,12,63:0:68:4  ./. ./.
RF01    280 .   A   C   0   .   AB=0.4;ABP=3.44459;AC=1;AF=0.1;AN=10;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=1.05263;EPP=3.0103;EPPR=4.58955;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=5;NUMALT=1;ODDS=6.90616;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=374;RO=22;RPL=1;RPP=3.0103;RPPR=4.58955;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=22;SRP=50.7827;SRR=0;TYPE=snp  GT:AD:AO:DP:PL:QA:QR:RO 0/0:7,0:0:7:0,21,109:0:119:7    0/0:2,0:0:2:0,6,32:0:34:2   0/1:3,2:2:5:17,0,33:34:51:3 ./. ./.
RF01    351 .   T   A   0   .   AB=0.4;ABP=3.87889;AC=2;AF=0.2;AN=10;AO=4;CIGAR=1X;DP=25;DPB=25;DPRA=1;EPP=11.6962;EPPR=3.94093;GTI=1;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=5;NUMALT=1;ODDS=8.27411;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=357;RO=21;RPL=0;RPP=11.6962;RPPR=3.94093;RPR=4;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=21;SRP=48.6112;SRR=0;TYPE=snp  GT:AD:AO:DP:PL:QA:QR:RO 0/1:3,2:2:5:17,0,33:34:51:3 0/0:4,0:0:4:0,12,63:0:68:4  0/0:7,0:0:7:0,21,109:0:119:7    ./. ./.