I'm super new to WGS and bioinformatics, but I'm a classic software data scientist, so I know enough to be annoying.
I'm using Platypus too call variants on 100X WGS via Nebula Genomics. I found an odd series of calls and am not sure if this is noise, or a mutation.
Is this a thing to investigate, or just junk?
Chr: chrX Position: 67631951-67631955 ID: . Reference: AGGGG* Alternate: TGGGT Qual: 160 Type: MNP Is Filtered Out: Yes - alleleBias Alleles: Alternate Alleles: TGGGT Allele Frequency: -1.0 Variant Attributes PP: 160 MMLQ: 35 TCR: 8 Mapping Quality: 44.97 NR: 0 HP: 4 HapScore: 1 FR: 0.5000 SbPval: 1.0 Source: # WE: 67631979 TC: 20 SC: TAGGCTGCTCAGGGGTCAGGG QD: 106.733937431 MGOF: 15 TCF: 12 BRF: 0.11 NF: 2 WS: 67631941 TR: 2