format_sumstats (tips)

usage: gsmap format_sumstats [-h] --sumstats SUMSTATS --out OUT [--snp SNP]
                             [--a1 A1] [--a2 A2] [--info INFO] [--beta BETA]
                             [--se SE] [--p P] [--frq FRQ] [--n N] [--z Z]
                             [--OR OR] [--se_OR SE_OR] [--chr CHR] [--pos POS]
                             [--dbsnp DBSNP] [--chunksize CHUNKSIZE]
                             [--format {gsMap,COJO}] [--info_min INFO_MIN]
                             [--maf_min MAF_MIN] [--keep_chr_pos]

Named Arguments

--sumstats

Path to gwas summary data

--out

Path to save the formatted gwas data

--snp

Name of snp column (if not a name that gsMap understands)

--a1

Name of effect allele column (if not a name that gsMap understands)

--a2

Name of none-effect allele column (if not a name that gsMap understands)

--info

Name of info column (if not a name that gsMap understands)

--beta

Name of gwas beta column (if not a name that gsMap understands).

--se

Name of gwas standar error of beta column (if not a name that gsMap understands)

--p

Name of p-value column (if not a name that gsMap understands)

--frq

Name of A1 ferquency column (if not a name that gsMap understands)

--n

Name of sample size column (if not a name that gsMap understands)

--z

Name of gwas Z-statistics column (if not a name that gsMap understands)

--OR

Name of gwas OR column (if not a name that gsMap understands)

--se_OR

Name of standar error of OR column (if not a name that gsMap understands)

--chr

Name of SNP chromosome column (if not a name that gsMap understands)

Default: 'Chr'

--pos

Name of SNP positions column (if not a name that gsMap understands)

Default: 'Pos'

--dbsnp

Path to reference dnsnp file

--chunksize

Chunk size for loading dbsnp file

Default: 1000000.0

--format

Possible choices: gsMap, COJO

Format of output data

Default: 'gsMap'

--info_min

Minimum INFO score.

Default: 0.9

--maf_min

Minimum MAF.

Default: 0.01

--keep_chr_pos

Keep SNP chromosome and position columns in the output data

Default: False