Indel realignment for 454 data
Hi, I'm now reanalyzing WGS data of some virus sequenced by 454. I want to identify SNPs using LoFreq. However, the indel realignment method of GATK is not working for 454 data. Is there any suggestion about the tools or methods that can replace this?
• 1,152 views
•
link
written
by
phongphak.06 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Assembly of chloroplast genome from plant WGS
written by adarsh •
-
SNP Calling using Genome Analysis Toolkit
written by Fid_o •
-
Indel realignment: GATK vs. BCFtools
written by martytriggers •
-
How to filter SNP and Indel under these criteria?
written by r00628112 •
-
GATK data-preprocessing omit Indelrealignment step
written by 9521ljh •
-
How to select SNPs the most conservative way after WGS Variant Calling?
written by serpalma.v •
-
The problem with sensitivity analysis of somatic variant caller
written by phongphak.06 •
-
How can identify the driver genes with germline mutations ?
written by andy7v9591 •
-
Very Large Insertion Detection Methodology Query
written by rob234king
-
Gatk Indel Realignment Taking Forever! Help
written by Ds89 •
Why it is not working? Does it throw any error message?
Have a look at ICC.
I got a message like 100% of my reads failing Platform454Filter. So when I take a look at GATK documentation I found this comment:
Because reads produced from the 454 technology inherently contain false indels, the realigner will not work with them (or with reads from similar technologies)