bam generated with bwa-meth

[PoisonAlien]

I aligned my Nome-seq reads with bwa-meth. Now I want to look at ndr and endogenous methylation. Following your protocol, I need to generate vcf. Does the bam file and index generated by bwa-meth compatible with biscuit ?

[wangyunpengbio]

It seems that I have encountered the sam problem.My script is:

biscuit pileup -r index/hg19.fa -i sams/SRR1282202.align.sort.bam -o SRR1282202.vcf -q 20
bgzip SRR1282202.vcf
tabix -p vcf SRR1282202.vcf.gz
biscuit vcf2bed -t hcg SRR1282202.vcf.gz > SRR1282202.hcg.bed &
biscuit vcf2bed -t gch SRR1282202.vcf.gz > SRR1282202.gch.bed &

And the result file(SRR1282202.hcg.bed and SRR1282202.gch.bed)contains nothing.### What's wrong with it?
However,using -t cg -t snp -t c ,I have got some results.

biscuit vcf2bed -k 10 -t cg SRR1282202.vcf.gz > SRR1282202.cg.bed
biscuit vcf2bed -k 10 -t snp SRR1282202.vcf.gz
biscuit vcf2bed -t c SRR1282202.vcf.gz > SRR1282202.c.bed

[shenhui1986]

Hi just letting everyone know that Wanding is currently away on vacation and won’t return until two weeks later. I doubt that he will receive these emails in China as gmail is blocked. I will give this a test next week and see what I find and report back to you. It’s a hectic week for me so perhaps will take a few days before I’ll be able to sit down and work on it. Thanks all! Thanks, Hui

…

____________________________________________________ Hui Shen, Ph.D. Assistant Professor, Van Andel Research Institute Center for Epigenetics Room 5004W 333 Bostwick Ave., N.E. Grand Rapids, Michigan 49503-2518 U S A Phone: 616-234-5362 Fax: 616-234-5562 email: hui.shen@vai.org https://shenlab.vai.org

____________________________________________________

On Aug 5, 2017, at 1:42 AM, wangyunpengbio ***@***.***> wrote: It seems that I have encountered the sam problem. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABTEUcNl2zcNZ-yr3bVRdnicgjQGwHTKks5sVADTgaJpZM4MN37P>.

[wangyunpengbio]

Thanks for your prompt action.Actually,when I use biscuit to generate bam file.I still the same result and don't get the HCG and GCH result.

biscuit align -t 12 index/hg19.fa fastq/SRR1282202_1.fastq.gz fastq/SRR1282202_2.fastq.gz | samtools sort -T . -O bam -o bams/SRR1282202.bam
samtools index bams/SRR1282202.bam
biscuit tview -g chr19:7525080 SRR1282202.bam index/hg19.fa
biscuit pileup -r index/hg19.fa -i SRR1282202.bam -o SRR1282202.vcf -q 20
bgzip SRR1282202.vcf
tabix -p vcf SRR1282202.vcf.gz

biscuit vcf2bed -k 10 -t cg SRR1282202.vcf.gz > SRR1282202.cg.bed &
biscuit vcf2bed -k 10 -t snp SRR1282202.vcf.gz > SRR1282202.snp.bed &
biscuit vcf2bed -t c SRR1282202.vcf.gz > SRR1282202.c.bed &
biscuit vcf2bed -t hcg SRR1282202.vcf.gz > SRR1282202.hcg.bed &
biscuit vcf2bed -t gch SRR1282202.vcf.gz > SRR1282202.gch.bed &

SRR1282202.c.bed ,SRR1282202.cg.bed and SRR1282202.snp.bed have result.
But SRR1282202.hcg.bed and SRR1282202.gch.bed are nothing in them.

System Information
Distributor ID: Ubuntu
Description: Ubuntu 16.04.2 LTS
Release: 16.04
Codename: xenial