Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post -specifying minimum read depth? Lspoor Bioinformatics 3 05-27-2013 02:20 AM
Samtools mpileup/bcftools cristae8 Bioinformatics 3 05-02-2012 01:43 PM
Read Depth in vcf (samtools / bcftools) Marie_Noir Bioinformatics 1 04-17-2012 07:48 AM
questions about samtools mpileup & bcftools chenjy Bioinformatics 0 07-26-2011 05:21 AM
Very high depth of coverage knott76 Bioinformatics 5 11-19-2009 01:27 AM

Thread Tools
Old 07-18-2012, 06:39 AM   #1
Andrew Beckerman
Junior Member
Location: Sheffield, UK

Join Date: Apr 2012
Posts: 5
Default Filter mpileup for high depth of coverage without bcftools/vcfutils


I am working with Illumina paired end read data, several populations. I am creating an mpileup from several .bam files, each from a different population. I would like to exclude candidate snp's where coverage in ANY one of the populations is ABOVE a read depth threshold.

To start, focusing on one scaffold, and just two of the populations, I would use

samtools mpileup -r scaffold_1 -D B1.20.bam D8.20.bam > s1B1D8.mpileup

Typically, I think one would now use the pipeline of mpileup and bcftools/ setting -D, as in varFilter -D 2000.

However, I need to retain an mpileup file.

I can use the -D option in mpileup to retain a column with some measure of the depth. However, it is not clear to me what it is with several samples, as it does not match exactly the minimum or average for the bam files included, and seems to only return a single value even with more than one bam.

Any ideas, suggestions and insight would be most appreciated.
Andrew Beckerman is offline   Reply With Quote
Old 07-19-2012, 01:24 AM   #2
Andrew Beckerman
Junior Member
Location: Sheffield, UK

Join Date: Apr 2012
Posts: 5

Perhaps a solution myself

# generate mpilup, say with two bams

samtools mpileup -B a.bam b.bam > out.mpileup

# Then use awk to filter on the depth of coverage columns (i.e. $4 and $7 for two bams)
# i.e. with a depth of 100 max in any depth column

awk '$4 <= 100 && $7 <= 100' out.mpileup > sifted.mpileup
Andrew Beckerman is offline   Reply With Quote

bcftools, depth of coverage, mpileup

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:22 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO