Quantcast
Channel: Post Feed
Viewing all articles
Browse latest Browse all 3147

Indel Left/Right Alignment

$
0
0

When matching indels between different VCF files (generated by different callers), there is this issue with left / right indel alignment, For example:

enter image description here

Here is a real example for one indel (from the same sample) called by:

Samtools --> 1 161047125 CTATA C

GATK --> 1 161047130 TATAG T

I know GATK has a small tool called "LeftAlignIndels" to solve this issue in the BAM files but I can't use it.

I am wondering if someone knows what is the indel alignment direction in samtools, GATK and Dindel? Is there an easy way to correct this at level of VCF files?

Thanks!


Viewing all articles
Browse latest Browse all 3147

Trending Articles