bcftools merge; retaining sample names

bcftools merge; retaining sample names

2

When I do bcftools merge, the headers do not retain the filenames.  How can I specify filenames?

This is my command 

bcftools merge vcf/unfiltered/*.vcf.gz -O z > msa/pooled.vcf.gz

However this is the relevant part of my header, despite the filenames I gave it.  Is it just up to me to parse the mergeCommand line? Or is there a way to use bcftools query to get the right headers after the fact?

##bcftools_mergeVersion=0.2.0-rc7-47-g02a1fb3+htslib-0.2.0-rc7-36-g6e2ebc4
##bcftools_mergeCommand=merge -O z vcf/unfiltered/lambda_virus.fasta.wgsim.fastq.gz-lambda_virus.vcf.gz vcf/unfiltered/lambda_virus.fasta.wgsim.fastq.gz-reference.vcf.gz vcf/unfiltered/sample1.fastq.gz-lambda_virus.vcf.gz vcf/unfiltered/sample1.fastq.gz-reference.vcf.gz vcf/unfiltered/sample2.fastq.gz-lambda_virus.vcf.gz vcf/unfiltered/sample2.fastq.gz-reference.vcf.gz vcf/unfiltered/sample3.fastq.gz-lambda_virus.vcf.gz vcf/unfiltered/sample3.fastq.gz-reference.vcf.gz vcf/unfiltered/sample4.fastq.gz-lambda_virus.vcf.gz vcf/unfiltered/sample4.fastq.gz-reference.vcf.gz 
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample1 2:Sample1       3:Sample1       4:Sample1       5:Sample1       6:Sample1       7:Sample1       8:Sample1       9:Sample1       10:Sample1


bcftools


samtools


merge


vcf

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