Question: IndelRealign mitochondrial DNA using b37
gravatar for Cindy
2.5 years ago by
Cindy20 wrote:

I want to run GATK IndelRealigner for mtDNA and use b37 indel reference as known sites. Here is my script. I got error for incompatible contigs. The NC_012920.1.fasta is mitochondria reference genome and includes only M contigs. How can I modify it to make it compatible to b37 indel reference genome? Thanks!

java  -jar GenomeAnalysisTK.jar \
         -R NC_012920.1.fasta \
     -T IndelRealigner \
     -targetIntervals file_GATKrealign.intervals \
     -I file \
      -o file_realn.bam \
      -known b37/1000G_phase1.indels.b37.vcf \
     -known b37/Mills_and_1000G_gold_standard.indels.b37.vcf

##### ERROR MESSAGE: Input files b37/1000G_phase1.indels.b37.vcf and reference have incompatible contigs. Please see more information. Error details: No overlapping contigs found.
##### ERROR   b37/1000G_phase1.indels.b37.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X]
##### ERROR   reference contigs = [M]
alignment • 946 views
ADD COMMENTlink modified 2.5 years ago by genomax74k • written 2.5 years ago by Cindy20
gravatar for Jeremy Leipzig
2.5 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

The problem is likely naming related (M vs MT) but the bigger issue is that this GATK realignment approach is really overkill for mitochondria sequences. You could easily do a real alignment using BLAST or something else more sensitive. There are no mitochondrial gold standard indels in your references anyway.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Jeremy Leipzig18k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 943 users visited in the last hour