Neandertals VCF file

Question

[khatami.mahshid]

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

[ATpoint]

What is the reference file?

[khatami.mahshid]

the refrence.fa is a hg19 human genome fasta file I download from UCSC.

[ATpoint]

...and the BAMs are on hg19 as well?

[khatami.mahshid]

yes they are. both refrence.fa and bam files are hg19.

Answer 1

[Pierre Lindenbaum]

bcftools call must be called after bcftools mpileup. See the manual : https://samtools.github.io/bcftools/howtos/variant-calling.html