about VCF and BAM files
2
1
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Bogdan ▴ 670
@bogdan-2367
Last seen 12 months ago
Palo Alto, CA, USA

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

SNV BAM • 2.4k views
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@martin-morgan-1513
Last seen 3 months ago
United States

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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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

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Bogdan ▴ 670
@bogdan-2367
Last seen 12 months ago
Palo Alto, CA, USA

Hi Martin ! thanks, very helpful ! we'll explore this way ! and hey ! ... looking forward to see you guys at Stanford in June !

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