Whole genome to whole exome data
0
0
Entering edit mode
19 months ago
MobiusT ▴ 20

I have a whole genome dataset in a bam file and want to convert a whole exome dataset. Which steps I should take?

whole-exome-sequencing whole-genome-sequencing • 909 views
ADD COMMENT
1
Entering edit mode

Do you mean that you have a bam file generated from WGS data and that you want to extract the exonic alignments? If so take a look into intersectBed.

ADD REPLY
0
Entering edit mode

While possible the solution from Pierre Lindenbaum will be much faster as (if the bam is sorted and indexed) samtools will use random access to pull the entries directly whereas intersect first needs to find them manually.

ADD REPLY
1
Entering edit mode
samtools view -M -L exome.bed -O BAM -o out.bam in.bam
ADD REPLY
0
Entering edit mode

This would be a theoretically equivalent dataset not a real exome dataset (since that generally uses capture techology).

ADD REPLY

Login before adding your answer.

Traffic: 1857 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6