Hi Sébastien, sorry that the error message is not clear enough. The parser (htslib) gives the warning [W::vcf_parse] FILTER 'NOCALL' is not defined in the header
which sometimes can be ignored, sometimes not. For merging, missing definitions are critical and `bcftools merge` should exit with a clearer error message. This will be fixed in the next release. Best wishes, Petr On Fri, 2015-07-03 at 12:51 +0200, Sébastien Letort wrote: > Hi, > > I've got 2 small vcf files that I want to merge. > > bcftools merge 002.vcf.gz 003.vcf.gz -O z -o merged.vcf.gz > The output is empty > > I had this warning, but I don't think it is linked to the problem > [W::vcf_parse] FILTER 'NOCALL' is not defined in the header > The filter not defined: NOCALL > > I tried not to use output option. > The last row is broken > chr2 212288942 COSM48361 T A 268.546 PASS > FDP=825;FR=.;FRO=825;FSRF=407;FSRR=418;FXX=0;QD=0.887096;RO=825;SRF=407;SRR=418;HS;OID=COSM48361;OPOS=212288942;OREF=T;OALT=A;OMAPALT=A;DP=2037;AO=0;FAO=0;FSAF=0;FSAR=0;FWDB=-0.0486189;HRUN=3;LEN=1;MLLD=360.134;R > > > Each input VCF seems ok. > bcftools view -H ../../vcfs/TSVC_variants_IonXpress_002.vcf.gz | wc -l > [W::vcf_parse] FILTER 'NOCALL' is not defined in the header > 200 > bcftools view -H ../../vcfs/TSVC_variants_IonXpress_003.vcf.gz | wc -l > [W::vcf_parse] FILTER 'NOCALL' is not defined in the header > 200 > > Here are the variant that cannot be merge in each input files > bcftools view -r chr2:212288942 002.vcf.gz -H > chr2 212288942 COSM48361 T A 182.964 PASS > AO=0;DP=825;FAO=0;FDP=825;FR=.;FRO=825;FSAF=0;FSAR=0;FSRF=407;FSRR=418;FWDB=-0.0391053;FXX=0;HRUN=3;LEN=1;MLLD=341.159;QD=0.887096;RBI=0.0401125;REFB=-4.33802e-06;REVB=-0.00893249;RO=825;SAF=0;SAR=0;SRF=407;SRR=418;SSEN=0;SSEP=0;SSSB=0;STB=0.5;TYPE=snp;VARB=0;HS;OID=COSM48361;OPOS=212288942;OREF=T;OALT=A;OMAPALT=A > > GT:GQ:DP:FDP:RO:FRO:AO:FAO:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR > 0/0:99:825:825:825:825:0:0:0:0:407:418:0:0:407:418 > > bcftools view -r chr2:212288942 003.vcf.gz -H > chr2 212288942 COSM48361 T A 268.546 PASS > AO=0;DP=1212;FAO=0;FDP=1211;FR=.;FRO=1211;FSAF=0;FSAR=0;FSRF=497;FSRR=714;FWDB=-0.0486189;FXX=0.000825076;HRUN=3;LEN=1;MLLD=360.134;QD=0.887022;RBI=0.0497906;REFB=-3.56957e-06;REVB=-0.0107378;RO=1211;SAF=0;SAR=0;SRF=497;SRR=714;SSEN=0;SSEP=0;SSSB=5.46104e-08;STB=0.5;TYPE=snp;VARB=0;HS;OID=COSM48361;OPOS=212288942;OREF=T;OALT=A;OMAPALT=A > > GT:GQ:DP:FDP:RO:FRO:AO:FAO:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR > 0/0:99:1212:1211:1211:1211:0:0:0:0:497:714:0:0:497:714 > > > Any idea of what happened ? > > You can download an archive with the file here > https://filex.univ-brest.fr/get?k=5YVOZXmUpDGm1gnrJVj > > cheer, > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
