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
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.