Hi,
I'm trying to run phaser pop example using the provided files, Whole_Blood.sample_map.txt and Whole_Blood.test_pairs.txt. I was able to download phASER_WASP_GTEx_v8_matrix.gw_phased.txt.gz from the GTEx website, but I'm having trouble locating the read-backed VCF file (phASER_GTEx_v8_merged.vcf.gz) despite having dbGAP access to phs000424. Is there a specific accession ID or version of phs000424 that I need to access to find the file?
Additionally, from my understanding, the phased vcf file only affects the results reported in columns 23-26 of the phaser_cis_var.py output (var_het_ref_counts, var_het_alt_counts, var_hom_hap1_counts, var_hom_hap2_counts) since the aFC-related measures in the other columns are calculated per variant rather than across all variants in the haplotype. Is this correct?
Hi, I'm trying to run phaser pop example using the provided files, Whole_Blood.sample_map.txt and Whole_Blood.test_pairs.txt. I was able to download phASER_WASP_GTEx_v8_matrix.gw_phased.txt.gz from the GTEx website, but I'm having trouble locating the read-backed VCF file (phASER_GTEx_v8_merged.vcf.gz) despite having dbGAP access to phs000424. Is there a specific accession ID or version of phs000424 that I need to access to find the file?
Additionally, from my understanding, the phased vcf file only affects the results reported in columns 23-26 of the phaser_cis_var.py output (var_het_ref_counts, var_het_alt_counts, var_hom_hap1_counts, var_hom_hap2_counts) since the aFC-related measures in the other columns are calculated per variant rather than across all variants in the haplotype. Is this correct?
Thank you so much!