Question: Bcftools merge sample order
0
gravatar for Chadi Saad
4 months ago by
Chadi Saad50
France
Chadi Saad50 wrote:

Does the sample names order in the multisample vcf file respect the input files order ?

for exemple: >> bcftools merge sample1.vcf sample2.vcf sample3.vcf

will always produce -->

CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sample1       sample2       sample3

?

ADD COMMENTlink modified 4 months ago by paolo002140 • written 4 months ago by Chadi Saad50
0
gravatar for paolo002
4 months ago by
paolo002140
paolo002140 wrote:

If you merge various vcf files into a single large vcf, the merged file will show the sample IDs names in the header in increasing order. The information in the hearder will follow the same order as in the separated files you provided as input. However, I guess be careful if there are not unique individuals and about the number of SNPs you have in the single vcf files in the input during your merging.

ADD COMMENTlink written 4 months ago by paolo002140
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