If I use igv interactively I can load a cram file, goto a position and click on that position to view the count details, including the numbers of alt and ref alleles which occur on each strand. I can use igv in batch mode to generate a snapshot showing the reads but I can't find a way to output the count details in text format, even though igv obviously knows them.
I just want some software that will do this in batch mode. It seems simple but I can't find anything which says it does this. I just want to specify a cram file and a position and for the program to tell me the counts for each allele on each strand.
All I can find is things that will tell me e.g. the total read depth, or total allele counts or allele balance. But I'd really like to see the counts by strand because if I see that there are reads supporting both alleles on both strands I'll feel more confident that the genotype call is valid.
Please can somebody point me at a solution. Thanks.
Coverage In Bam File - Bases And Overall Count
Counting Read Support At A Particular Position Of A Bam File
Finding all bases at a specific genomic position
Nucletotide distribution, at each position, in a .sam/.bam file ?
etc...
Thanks. So to get the strand-specific information it looks like I need a tool called bam-readcount, which is available here: https://github.com/genome/bam-readcount