credtools qc

Run quality control on locus-level summary statistics and LD matrices.

credtools qc INPUTS OUTDIR [OPTIONS]

Common Use

credtools qc work/chunks/loci_list.txt work/qc --threads 4

With outlier removal:

credtools qc work/chunks/loci_list.txt work/qc_cleaned \
  --threads 4 \
  --remove-outlier

Options

Option	Meaning	Default
--threads	worker count	1
--remove-outlier	remove outliers and rerun QC on cleaned data	off
--logLR-threshold	LD mismatch threshold	2.0
--z-threshold	z-score threshold	2.0
--z-std-diff-threshold	marginal SNP outlier threshold	3.0
--r-threshold	correlation threshold with lead SNP	0.8
--dentist-pvalue-threshold	Dentist-S -log10(p) threshold	4.0
--dentist-r2-threshold	Dentist-S LD threshold	0.6
--enable-c1b	enable high-z residual rule	off
--c1b-z-std-diff-threshold	C1b residual threshold	10.0
--adaptive-qc	run two-stage adaptive QC	off
--adaptive-lambda-threshold	adaptive QC lambda-s trigger	0.05
--log-file	write logs to a file	none

Outputs

OUTDIR/
- qc.txt.gz
- qc_run_summary.log
- {locus_id}/
- cleaned/

If cleaned files are created, use:

OUTDIR/cleaned/cleaned_loci_info.txt.gz

as the next input for finemap.