Zeta Mui

Failed to complete command task: 'getAlignmentStats_generateStats_000'

3

I am running manta 1.6.0 with alignment output from STAR-Fusion's Aligned.out.sam after it is compressed to bam and sorted. The manta options for the configManta.py I used was `--rna --bam...

Unexpectedly high log2 ratios for some but not all samples

2

I have tried to compare the samples with or without this issue but couldn't find anything that could be the reason. Apart from ploidy # are there other reasons that...

BAM after MarkDuplicates with Picard produces different CNV calling results with BAM that has the duplicates *removed* with Picard

2

Used version: 0.9.1 We have an established pipeline and we have always used the BAM file with duplicates marked with Picard. However, a while ago, we were analysing 2 sequenced...