Question: ref and alt allele count from BAM file
0
gravatar for monaallouba
11 months ago by
monaallouba0 wrote:

Hi All,

I would like to calculate the allele ratio of ref/alt at a specific position. How can I determine the ref and alt counts from the BAM file? (or is it better to extract this info from the VCF?)

Thank you

rna-seq allele_count bam • 516 views
ADD COMMENTlink modified 11 months ago by Vitis2.3k • written 11 months ago by monaallouba0
0
gravatar for Vitis
11 months ago by
Vitis2.3k
New York
Vitis2.3k wrote:

Both BAM and VCF can be used for this. In VCF, you would be looking for the values in the AD field for each sample. For BAM, you may want to consider using PySAM's pileup engine to query the position and reads stacked at that position. Just be careful with indels when using PySAM, you'll have to add special code to distinguish no coverage and deletions at these positions.

To tap into VCF, use PyVCF

https://pyvcf.readthedocs.io/en/latest/

To tap into BAM, use PySAM

https://pysam.readthedocs.io/en/latest/

ADD COMMENTlink written 11 months ago by Vitis2.3k
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