Down-sample to one read per SNP loci per sample
Does anyone know if there is a way of downsampling to a coverage of 1x per sample at known SNP loci? I have tried GATK downsample but receive an error that the lower limit is 200x per SNP.
After aligning and SNP calling using a combination of high and low coverage samples I would like to take the called SNP loci and randomly sample one read per loci per sample.
• 1,806 views
•
link
written
by
aylward.megan •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Dealing with variable sequencing depth.
written by a •
-
Which SNP callers are suitable for QTL mapping in GBS experiments with low coverage?
written by rimgubaev
-
Calling SNPs with low coverage
written by devin.porter92 •
-
Substituting heterozygous sites by randomly sampling one allele
written by outlier95 •
-
BWA mem few reads align
written by aylward.megan •
-
Forum: Multisample SNP/SNV calling - What's your favourite method?
written by amcrisan
-
Downsampling By Having A Ceiling On Number Of Reads At Each Site
written by caina89 •
-
Pcr Free Variant Calls
written by tommy.carstensen •
-
Why Ts/Tv Decreases With High Mq Values?
written by isp2 •
-
Variation & Genotype Calling From Ngs Data - Per Sample Or Multi Sample?
written by Travis
