Hi all,
I have Bam files of Neandertals from UCSC database. I tried to convert these bam files to VCF files with samtools mpileup and bcftools mpileup . but what I received is like these :
chr10 298350 . C <*> 0 . DP=1 PL 0,3,22
chr10 298351 . A <*> 0 . DP=1 PL 0,3,20
chr10 306039 . C T,<*> 0 . DP=1 PL 15,3,0,15,3,15
chr10 306040 . C <*> 0 . DP=1 PL 0,3,15
chr10 306041 . G <*> 0 . DP=1 PL 0,3,21
chr10 306042 . G <*> 0 . DP=1 PL 0,3,17
chr10 306043 . G <*> 0 . DP=1 PL 0,3,20
The "ALT" column is <*> and the "Quality" is 0 for all rows. it also doesn't have genotype like "0/1".
what is the problem?
the command I used is this:
samtools mpileup -v -u -f refrence.fa SLFeld1.hg19.bam > variants.vcf
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written
by
khatami.mahshid •
1 answer
bcftools call must be called after bcftools mpileup. See the manual : https://samtools.github.io/bcftools/howtos/variant-calling.html
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What is the reference file?
the refrence.fa is a hg19 human genome fasta file I download from UCSC.
...and the BAMs are on hg19 as well?
yes they are. both refrence.fa and bam files are hg19.