Best (GATK compatible) RadSeq/GBS pipeline in 2021
0
0
Entering edit mode
6 months ago
William ★ 4.9k

What is the best RadSeq/GBS pipeline in 2021?

Some of the tings that I am looking for in a GBS pipeline are:

  1. can be used with a reference genome
  2. automatic detection of enzyme / restriction sites used per sample (for the correct in-sillico digestion of the reference genome)
  3. can output standard BAM files
  4. can output GVCF files that can used together in GATK to do joint variant calling together with WGS GVCF files

Or is it maybe possible (with some tweaking of arguments and pre/post processing of data) to pull RadSeq/GBS data trough a BWA+GATK pipeline and still get good results?

Thank you.

radseq gbs gatk • 276 views
ADD COMMENT
0
Entering edit mode

Just processing RadSeq/GBS as 'faulty' WGS data did not seem to work. This results is c.a. 33% less TruePositive HOM_VAR SNPs, compared to a dedicated RadSeq/GBS pipeline and a benchmark WGS sample. So these RadSeq/GBS pipelines do do something useful to achieve better variant calling results. . My main guess is in-silico digestion of the reference genome with the relevant restriction enzyme.
Still am interested in a RadSeq/GBS pipeline that can output GATK compatible GVCF files.

ADD REPLY

Login before adding your answer.

Traffic: 1215 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