Question: Neandertals VCF file
0
gravatar for khatami.mahshid
12 months ago by
khatami.mahshid20 wrote:

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
snp • 276 views
ADD COMMENTlink modified 12 months ago by Pierre Lindenbaum130k • written 12 months ago by khatami.mahshid20

What is the reference file?

ADD REPLYlink written 12 months ago by ATpoint38k

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

ADD REPLYlink written 12 months ago by khatami.mahshid20

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

ADD REPLYlink written 12 months ago by ATpoint38k

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

ADD REPLYlink written 12 months ago by khatami.mahshid20
3
gravatar for Pierre Lindenbaum
12 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

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

ADD COMMENTlink written 12 months ago by Pierre Lindenbaum130k
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