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)
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