Question: about VCF and BAM files
1
gravatar for Bogdan
2.7 years ago by
Bogdan530
Palo Alto, CA, USA
Bogdan530 wrote:

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

bam snv • 924 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Bogdan530
Answer: A: about VCF and BAM files
2
gravatar for Martin Morgan
2.7 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

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.

 

ADD COMMENTlink written 2.7 years ago by Martin Morgan ♦♦ 22k

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

ADD REPLYlink written 21 months ago by Bogdan530
Answer: A: about VCF and BAM files
0
gravatar for Bogdan
2.7 years ago by
Bogdan530
Palo Alto, CA, USA
Bogdan530 wrote:

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

ADD COMMENTlink written 2.7 years ago by Bogdan530
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