This looks like an edge case that may be related to phaser itself or underlying code in this repository.
t
Scenario: Five consecutive calls from two independent but consecutive block substitutions followed by a single SNV
Sample in question: MMRF_2787_1_PB_WBC_C3_KHS5U-MMRF_2787_1_BM_CD138pos_T1_KHS5U.bwa.strelka2.pass.vcf.gz
PASS VCF CALLS:
chr2 88860919 . T A
chr2 88860920 . G A
chr2 88860921 . A G
chr2 88860922 . G C
chr2 88860923 . C T
Post PREP OUTPUT:
chr2 88860919 . TGC AAT (## The "C" is not a ref allele, this is the main issue)
chr2 88860921 . AG GC
Based on the image below the correct output should be:
chr2 88860919 . TG AA
chr2 88860921 . AG GC
chr2 88860923 . C T
It Actually looks like the resulting call that is causing the issue is trying to phase the blocksub and SNV, as they look phased which should have provided a call like
chr 88860919 . TGagC AAagT
its like we stripped out the two ref bases shown in lower case
bug fixed. Phased Variants were captured together even if locations were not consecutive. The capture of blocks has been revisited for non-consecutive phased variants.
This looks like an edge case that may be related to phaser itself or underlying code in this repository. t Scenario: Five consecutive calls from two independent but consecutive block substitutions followed by a single SNV
Sample in question: MMRF_2787_1_PB_WBC_C3_KHS5U-MMRF_2787_1_BM_CD138pos_T1_KHS5U.bwa.strelka2.pass.vcf.gz
PASS VCF CALLS: chr2 88860919 . T A chr2 88860920 . G A chr2 88860921 . A G chr2 88860922 . G C chr2 88860923 . C T
Post PREP OUTPUT: chr2 88860919 . TGC AAT (## The "C" is not a ref allele, this is the main issue) chr2 88860921 . AG GC
Based on the image below the correct output should be: chr2 88860919 . TG AA chr2 88860921 . AG GC chr2 88860923 . C T
It Actually looks like the resulting call that is causing the issue is trying to phase the blocksub and SNV, as they look phased which should have provided a call like chr 88860919 . TGagC AAagT
its like we stripped out the two ref bases shown in lower case