Question: Get Allele Frequency of each SNP in RNASeq
0
gravatar for a1249m
4.0 years ago by
a1249m0
European Union
a1249m0 wrote:

For a set of RNASeq bam files aligned to hg19, I would like to calculate the number of reads mapping to all possible (high-confidence) alleles for each position. What is the best way to do this? I have tried using samtools mpileup and bcftools as was recommended in a few solutions Extract Allele At Particular Positions From Bam Files, but the output either gives me 'Error: Could not parse --min-ac g', or gives a vcf file which is deprecated and shows me a vcf file whose output I am not sure is correct. Here is a sample:

chr2    100002198       .       T       .       32.9952 .       DP=1;MQ0F=0;AF1=0;AC1=0;DP4=1,0,0,0;MQ=60;FQ=-29.991    GT:PL:DV        0/0:0:0

chr2    100002199       .       A       .       32.9952 .       DP=1;MQ0F=0;AF1=0;AC1=0;DP4=1,0,0,0;MQ=60;FQ=-29.991    GT:PL:DV        0/0:0:0

chr2    100002200       .       T       .       32.9955 .       DP=1;MQ0F=0;AF1=0;AC1=0;DP4=1,0,0,0;MQ=60;FQ=-29.9906   GT:PL:DV        0/0:0:0

chr2    100002201       .       C       .       32.9955 .       DP=1;MQ0F=0;AF1=0;AC1=0;DP4=1,0,0,0;MQ=60;FQ=-29.9906   GT:PL:DV        0/0:0:0

 

What I need is a file that shows me 1) each base position, 2) the reference nucleotide at that position, 3) the range of alleles shown by my sample at that position, and 4) the frequency of each allele.

sequencing snp rna-seq • 1.6k views
ADD COMMENTlink modified 4.0 years ago by Chris Miller20k • written 4.0 years ago by a1249m0
0
gravatar for mark.ziemann
4.0 years ago by
mark.ziemann1.1k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.1k wrote:

I can't help you with the bcftools error, but I have done something similar using VarScan which worked nicely.

ADD COMMENTlink written 4.0 years ago by mark.ziemann1.1k
0
gravatar for Chris Miller
4.0 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

If you know the positions that you want to query, bam-readcount is probably the tool you're looking for.(https://github.com/genome/bam-readcount)

ADD COMMENTlink written 4.0 years ago by Chris Miller20k

Thanks Chris, this what I was looking but I got confused from the documentation about the format of regions file. Can you please explain the right format it accepts?

ADD REPLYlink written 3.1 years ago by fizer20

Tab-delimited, one based coordinates

1    1234   1234
17   9876  9876

Column 4+ will be ignored

ADD REPLYlink written 3.1 years ago by Chris Miller20k
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