hello,

I have a couple of VCF files I would like to join for multi-sample SNP calling.

I use BCFtools merge

    ##bcftools_mergeVersion=1.4.1+htslib-1.4.1
##bcftools_mergeCommand=merge --force-samples sample1.bam.vcf.gz sample2.bam.vcf.gz; Date=Mon May 29 09:58:15 2017
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  unknown 2:unknown
CG_Chr01    200 .   C   A   70.2067 .

However when everything is done the samples are all called "unknown"

this is kind of a problem for me down the road( i have a total of 24 samples) so i would like to include the original sample names in the vcf file.

I also have used the --file-list <file> option. This gives the same result.

When I use " --use-header" option I get the next error message "Segmentation fault (core dumped)"

Could someone point me in the right direction to fix this problem for me?

-edit 30/05/2017

I found out that my fastaq files don't have readsgroup.

using Picard AddOrReplaceReadGroups i assigned sample names and when i merge those files in a later step i get to see the sample names i used.

Hope this helps someone in the future. :)

hint.

if samtools view -H /path/to/my.bam | grep '^@RG' shows noting then use the step above.

Regards,

Covux