Best Tools for analyzing Bisulfite sequencing bam files?

Question

[Jon17]

Once you have aligned bam file for Bisulfite sequencing what are the top tools for analyzing the alignments?

bismark_methylation_extractor is one, what else?

Answer 1

[dariober]

I've written a methylation extractor, bam2methylation, which I don't claim to be a top tool, just a tool.

[Jon17]

Thankyou, i'm downloading it now.

[Jon17]

Is it throwing an error?

bioinformatics-cafe/bam2methylation.py --input sample1.proper.bam --ref /data1/nimblegen-pipeline/nimblegensoftware/config/epi-reference/hg19_chrY_PARs_masked.fa

Methylation file: /tmp/tmp_bam2methylation_vUMnk8/read-F128.mpileup.txt samtools view -u -F128 sample1.proper.bam | samtools mpileup -d100000000 -Q0 -B -f /data1/nimblegen-pipeline/nimblegen-software/config/epi-reference/hg19_chrY_PARs_masked.fa - | sort -k1,1 -s Methylation file: /tmp/tmp_bam2methylation_vUMnk8/read-f128.mpileup.txt samtools view -u -f128 sample1.proper.bam | samtools mpileup -d100000000 -Q0 -B -f /data1/nimblegen-pipeline/nimblegen-software/config/epi-reference/hg19_chrY_PARs_masked.fa - | sort -k1,1 -s sort -m -s -k1,1 -k2,2n -k3,3n /tmp/tmp_bam2methylation_vUMnk8/read-F128.mpileup.txt /tmp/tmp_bam2methylation_vUMnk8/read-f128.mpileup.txt | bedtools groupby -g 1,2,3 -c 5,6,7 -o sum,sum,distinct | awk '{if($4==0 && $5==0){pct= 0} else {pct= 100*($4/$5)} printf("%s
%s %s %0.2f %s %s %s\n", $1, $2, $3, pct, $4, $5, $6)}'

[dariober]

It looks fine. It's printing what is being executed.