How to keep sample name while using samtools mpileup + varscan to do variant call?

Question

[MatthewP]

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.

[ATpoint]

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

Answer 1

[Pierre Lindenbaum]

http://varscan.sourceforge.net/germline-calling.html

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.

[KOfori]

In creating the multisample mpileup with SAMtools for subsequent variant calling with Varscan2, did you populate the Bamlist file as alternating normal - tumor pairs or the sequence doesn't matter?

Eg, Bamlist.txt with each sample on a separate line:

NA1230-norm.bam
NA1230-tumor.bam
NA1231-norm.bam
NA1231-tumor.bam