Dear all,
please could you advise : considering a VCF file (and a specific position of a mutation), and a BAM file, what package or function I could use in BioC that will count the reads on FORWARD and REVERSE STRAND, for REFERENCE and ALTERNATE alleles ? thanks !
-- bogdan
You can use Rsamtools::pileup() to create a tally of relevant positions, e.g.,
library(Rsamtools)
example(scanBam, echo=FALSE) # points to ex1.bam sample file
sbp = ScanBamParam(which=GRanges("seq1", IRanges(c(100, 200), width=1)))
pileup(fl, scanBamParam=sbp)
The VCF could be input from VariantAnnotation::readVcf(), maybe using ScanVcfParam to restrict input to particular fields.
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version 2.3.6
Dear Martin, thank you again for pointing us into the direction of using Rsamtools library. I will repost a similar question, as the output we would like to have would be :
CHR
position
refAllele
altAllele
refCount
altCount
totalCount
chr19
61766
A
C
36
10
46
chr19
61774
A
G
40
9
49
chr19
61799
T
G
43
7
50
chr19
62155
A
G
49
11
60
chr19
71178
G
C
3
8
11
chr19
80384
C
A
6
10
16