Question: Indel Left/Right Alignment
gravatar for sa9
5.0 years ago by
USA, Cambridge
sa9780 wrote:

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?


indel • 6.0k views
ADD COMMENTlink modified 2.4 years ago by Erik Garrison2.0k • written 5.0 years ago by sa9780
gravatar for lh3
5.0 years ago by
United States
lh330k wrote:

For NGS analysis, the convention is to left align indels. To use GATK and samtools, you should use an aligner that left aligns indels; otherwise at least samtools will have worse performance and accuracy. It is too late to fix the issue in VCF.

EDIT: wait.. In your example, the two callers deleted different bases. The two calls are intrinsically different. You cannot move the indel to make them the same.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by lh330k
gravatar for pd3
5.0 years ago by
pd3310 wrote:

There is the "vcf norm" tool in htscmd which left-aligns and normalizes indels in VCFs. It can be downloaded from github, google for 'htslib'.

ADD COMMENTlink written 5.0 years ago by pd3310

Thanks Ixe, we used similar tool from GATK specifically for VCF files ( but as lh3 pointed out, it is too late to correct in the VCF file.

ADD REPLYlink written 5.0 years ago by sa9780
gravatar for Erik Garrison
2.4 years ago by
Erik Garrison2.0k
Somerville, MA
Erik Garrison2.0k wrote:

I suggest taking a look at vt: It includes a very nice left alignment routine. They've got a nice paper describing the method for normalizing the representation:

ADD COMMENTlink written 2.4 years ago by Erik Garrison2.0k

Thanks Erik. Vt is awesome. We have been using it for couple of months now.

ADD REPLYlink modified 21 months ago • written 2.4 years ago by sa9780
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