Like I said, I ran the command without output options to have merged.vcf on stdout. And this way I could see the broken row.
Sébastien Le 03-07-2015 15:36, Thomas W. Blackwell a écrit : > I would put the command line flags before the input file names: > > bcftools merge -O z -o merged.vcf.gz 002.vcf.gz 003.vcf.gz > > - tom blackwell - > > On Fri, 3 Jul 2015, S�bastien 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, > > -- > Sébastien Letort - bio-informaticien > Inserm U1078, Génétique, Génomique fonctionnelle et Biotechnologies > 46 rue Félix Le Dantec > CS 51819 > 29218 BREST CEDEX 2 > Tel. 02.98.22.34.08 (EFS) > Tel. 02.98.01.82.37 (UBO) > > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ 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
