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make_snp_file.py, includevep, AND, OR

Status: Open.

#19 In mhguo1/TRAPD;

· Elliott77 opened on Aug 25, 2021

Not so good result for TRAPD

Status: Open.

#18 In mhguo1/TRAPD;

· gevin-MB opened on Jul 27, 2021

count_control file gives same output regardless of arguments or input types

Status: Open.

#17 In mhguo1/TRAPD;

· Kaskere opened on Jul 2, 2021

bug in make_snp_file.py

Status: Open.

#15 In mhguo1/TRAPD;

· weizhu365 opened on Jul 28, 2020

Possibility to subset genes prior to the burden test

Status: Open.

#14 In mhguo1/TRAPD;

· dalmiaa opened on Jul 16, 2020

inconsistent results

Status: Open.

#13 In mhguo1/TRAPD;

· quentin67100 opened on Mar 17, 2020

Genes on chrX (i.e. _AR_) have zero hom and het counts in step 2b)

Status: Open.

#12 In mhguo1/TRAPD;

· dioncst opened on Feb 18, 2020

Shell in the README is wrong

Status: Open.

#11 In mhguo1/TRAPD;

· CancerGenome opened on Jan 20, 2020

--pop option with gnomad r.2 data

Status: Open.

#10 In mhguo1/TRAPD;

· jenkelly10 opened on Jan 2, 2020

SNPEFF_GENENAME not available for SnpEff annotated vcf

Status: Open.

#9 In mhguo1/TRAPD;

· ScubaChris opened on Nov 13, 2019

vep_annotation

Status: Open.

#8 In mhguo1/TRAPD;

· asura117 opened on Jun 27, 2019

MAF and AF

Status: Open.

#7 In mhguo1/TRAPD;

· sureyana956 opened on Jun 6, 2019