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Liftovered b37 to hg19 somatic PON resource

Status: Open.

#18 In cgpu/sarek;

· cgpu opened on Mar 5, 2020

Replace FASTQC with fastp

Status: Open.

#15 In cgpu/sarek;

· cgpu opened on Jan 3, 2020

seed length

Status: Open.

#14 In cgpu/sarek;

· cgpu opened on Jan 3, 2020

Safely split reads

Status: Open.

#13 In cgpu/sarek;

· cgpu opened on Jan 3, 2020

FASTQ to uBAM takes a long time! (5hours)

Status: Open.

#12 In cgpu/sarek;

· cgpu opened on Jan 1, 2020

bed file vs intervals coordinate system

Status: Open.

#11 In cgpu/sarek;

· cgpu opened on Dec 31, 2019

HapCall: Consider adding -forceActive and -dontTrimActiveRegions simultaneously to reduce false negatives

Status: Open.

#10 In cgpu/sarek;

· cgpu opened on Dec 30, 2019

:caution: "HaplotypeCaller does not call variant depending on the interval list I use"

Status: Open.

#9 In cgpu/sarek;

· cgpu opened on Dec 30, 2019

MarkDuplicatesSpark: consider adding --conf 'spark.local.dir=./tmp

Status: Open.

#6 In cgpu/sarek;

· cgpu opened on Dec 9, 2019

Benchmark execution time + cost of using EstimateLibraryComplexity seperately instead of writing a metrics file in MarkDuplicatesSpark

Status: Open.

#5 In cgpu/sarek;

· cgpu opened on Dec 8, 2019

MarkDuplicateSpark is slower than normal MarkDuplicates - solution: omit -M

Status: Open.

#4 In cgpu/sarek;

· cgpu opened on Dec 8, 2019

bwa mem | samtools sort hybrid command introduces inefficiency ( up to 3x longer runtime)

Status: Open.

#3 In cgpu/sarek;

· cgpu opened on Dec 4, 2019