Dear community Using the GATK's tools "haplotypecaller" and "ASEReadCounter" it is possible to produce a vcf file and a tabulated file for allele specific expression …
I ran the GATK tool ASEReadCounter to measure allele specific expression (ASE). There were 100 BAM input files processeced by ASEReadCounter. The output (ASE file) …
For those familiar with GATK, FastaAlternateReferenceMaker (unless the --useIUPAC flag is added) always uses the alternate allele at heterozygous SNP sites. I would like to …
Can you clarify (with an example) how your data looks like and how you obtained it?