Question: How to keep sample name while using samtools mpileup + varscan to do variant call?
gravatar for MatthewP
19 months ago by
MatthewP390 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 • 941 views
ADD COMMENTlink modified 19 months ago by Pierre Lindenbaum126k • written 19 months ago by MatthewP390

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

ADD REPLYlink written 19 months ago by ATpoint29k
gravatar for Pierre Lindenbaum
19 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k 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 19 months ago by Pierre Lindenbaum126k
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