STAR genomeConsensusFile description
0
0
Entering edit mode
8 weeks ago
chasem ▴ 50

In the STAR 2.7 docs, this setting is defined:

14.4 Genome Parameters
...
--genomeConsensusFile
default: -
string: VCF file with consensus SNPs (i.e. alternative allele is the major
(AF>0.5) allele)

But I am unsure of what this looks like, exactly. If there are for instance 4000 samples, presumably I wouldn't need to keep all of those samples in the VCF after filtering for sites with minor allele freq > .5? Would one just randomly select a sample to keep, in this case?

A follow on to this -- how does using the --genomeConsensusFile affect --varVCFfile, which are variants for a specific sample, if at all? Is it unnecessary to use genomeConsensusFile if using varVCFfile?

Finally, which one of these (maybe both? maybe neither?) affect behavior when seeting --waspOutputMode?

14.24 WASP parameters
--waspOutputMode
default: None
string: WASP allele-specific output type. This is re-implemenation of the
original WASP mappability filtering by Bryce van de Geijn, Graham McVicker,
Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper:
Nature Methods 12, 1061–1063 (2015),
https://www.nature.com/articles/nmeth.3582 .
SAMtag
add WASP tags to the alignments that pass WASP filtering
personal_variant alignment star • 146 views
ADD COMMENT

Login before adding your answer.

Traffic: 1518 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