Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
bcftools doesn't call suspected indel rwmills Bioinformatics 3 10-05-2015 10:43 AM
VarScan somatic indel caller working incorrectly? ElenaN Bioinformatics 1 03-03-2014 02:31 AM
VarScan mpileup2snp missing a call - can't figure out why eeyun Bioinformatics 3 10-01-2013 02:59 PM
VarScan mpileup2snp --p-value affects genotype call Graham Etherington Bioinformatics 2 10-22-2012 01:41 PM
samtools indel call method? Alex Renwick Bioinformatics 3 08-31-2012 06:50 AM

Thread Tools
Old 11-27-2015, 04:13 AM   #1
Location: US

Join Date: Feb 2011
Posts: 24
Default call indel and SNP by varscan

Hi all,

I met problem when I work on a 7M bacterium genome. I mapped 140x of paired-end reads (151x2) from illumina to a Pacbio reference genome by BWA mem. Then used samtool to get a mpileup file. Finally using varscan to call indel and SNP. Below is commands I used:

$bwa mem -M -t 6 Pacbio_ref reads_1.fq reads_2.fq | samtools view -buS - | samtools sort - illumina_paired_map_pacbio.sorted
$samtools index illumina_paired_map_pacbio.sorted.bam

get mpileup
$samtools mpileup -f Pacbio_ref.fastq illumina_paired_map_pacbio.sorted.bam > mpileup_output
call SNP
java -Xmx6g -jar VarScan.v2.3.9.jar  \
mpileup2snp mpileup_output \
--min-coverage 20  \
--min-reads2 2 \
--min-avg-.01 \
--p-value 0.05  \
--output-vcf 1 > 05snp.vcf
After that, I got only 268 SNP, similar work for indel but only 78 were found.

I don't think those numbers should be so low. Would you please help to check if there is anything wrong on any step? I think maybe the parameters in BWA were not set correctly. Please help!

doublealice is offline   Reply With Quote
Old 12-03-2015, 09:32 AM   #2
Jane M
Senior Member
Location: Paris

Join Date: Aug 2011
Posts: 237

Don't know if it can solve your problem but you can try to add -B option to samtools mpileup, as discussed here for example:
Jane M is offline   Reply With Quote

bwa, samtools, snp, varscan

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 12:31 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO