Question: Base call from BAM file
0
gravatar for Simo
14 months ago by
Simo30
Italy
Simo30 wrote:

Hi, I have a BAM file and a reference (let's say 1000 genomes data), I would like to extract from the BAM file all the possible overlapping bases with my reference dataset (not only the variants. Basically I would like to perform a base calling and not a variant calling). This extraction should be done according to a random selection of one read per base. Is there any way to do it?

Thanks

bam vcf • 510 views
ADD COMMENTlink written 14 months ago by Simo30

You could pipe the output of samtools mpileup to a script that randomly selects a single base (no clue why you'd want to do that).

ADD REPLYlink written 14 months ago by Devon Ryan80k

all the possible overlapping bases with my reference dataset

How do you define indel overlap?

I would like to perform a base calling and not a variant calling

How does this differ from setting the flag on your favorite variant caller to also output homozygous reference calls?

This extraction should be done according to a random selection of one read per base.

Why are you downsampling? Why aren't you extracting all read bases that align to any given position and processing that?

ADD REPLYlink written 14 months ago by d-cameron1.8k
  • I do not take into account indels.

  • I don't have any experience on this, that's why I was asking for help.

  • I'm working on a low coverage aDNA.

Thanks

ADD REPLYlink written 14 months ago by Simo30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1370 users visited in the last hour