Question: How to keep sample name while using samtools mpileup + varscan to do variant call?
gravatar for MatthewP
8 months ago by
MatthewP80 wrote:

Hello, everyone. I am using samtools mpileup and varscan to do variant call, but this will lost all the sample names. For example if I have 10 bam file name like 18R07049.bam ... 18R07058.bam, I pileup them all to 18R07.mpileup:

samtools mpileup -f myref.fasta -o 18R07.mpileup *.bam

Then use varscan mpileup2cns:

java -jar varscan.jar mpileup2cns 18R07.mpileup --output-vcf 1 > 18R07.vcf

When I checked 18R07.vcf i found it lost all the sample names, and become:

sample1 sample2 ... sample10

Then I tried not to mpileup all file to one file, I mpileup them separately and varscan mpileup2cns one by one, still it lost all sample names. I want to know how can I keep those sample names? thanks everyone.

mpileup samtools varscan • 479 views
ADD COMMENTlink modified 8 months ago by Pierre Lindenbaum118k • written 8 months ago by MatthewP80

Why don't you simply awk them into the VCF when the process is finished?

ADD REPLYlink written 8 months ago by ATpoint14k
gravatar for Pierre Lindenbaum
8 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

As of v2.3.1, you can provide a list of sample names to use in the VCF header with the --vcf-sample-list parameter. This list should be in plain text, one sample per line, in the order that samples appear in the raw mpileup input.

ADD COMMENTlink written 8 months ago by Pierre Lindenbaum118k
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