phaser_gene_ae output with 0 Count?

[deb0612]

When running "python ~/tools/phaser/phaser_gene_ae/phaser_gene_ae.py -- tast_case.haplotypic_counts.txt --features gencode.v19.GRCh37.genes.bed --o phaser_test_case_gene_ae.txt" command, the output file show 0 aCount, bCount and totalCount.

I checked the input haplotypic_counts file, and it show the Count number.

[secastel]

This is because the chromosome naming between the files going into phaser.py and the gene annotation file you are using for phaser_gene_ae.py. I can see that you don't have "chr" in the name of the contig for the gene annotation file, which doesn't match the outputs from phaser. Chromosome names must match or all counts will show up as 0, which is what you are seeing here.