run the following command for an up-to-date help message and an overview of all commands:
python bedmerger.py -h
requires plink 1.9, numpy and pandas, on spudhead/spudlings, run using python 2.7.6
logging is very messy and not consistent
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from the human origins data set, get all snp on chromosome X that have an ancestral allele typed
python bedmerger.py --bed /data/external_public/human_origins_affy/EuropeFullyPublic/vdata \ --check-reference \ --reference_path ancestral_hg19 \ --keep_snp_id false \ --out out/vdata_polarized \ --chromosome X \ --twd tmp \ --plink ~/bin/plink -
merge the data sets from bhakar2013 ,the human origins data set and 1000g, check the reference and keep only snp present in all three data sets, write a vcf file in the end
python bedmerger.py --vcf /data/external_public/1000genomes/release/Phase3/ALL.chr21.phase3_shapeit2_mvncall_integrated.20130502.genotype.vcf.gz \ --bed /data/external_public/human_origins_affy/EuropeFullyPublic/vdata \ --bed /data/external_public/behar_et_al_2013/new_data_in_paper \ --check-reference \ --reference_path hg19 \ --keep_snp_id false \ --chromosome 21 \ --twd tmp \ --plink ~/bin/plink \ --merge_type inner \ --output_type vcf -
merge the data sets from bhakar2013 and the human origins data set, keep all snp and set missing data to the reference allele
python bedmerger.py --bed /data/external_public/human_origins_affy/EuropeFullyPublic/vdata \ --bed /data/external_public/behar_et_al_2013/new_data_in_paper \ --check-reference \ --reference_path hg19 \ --keep_snp_id false \ --twd tmp \ --merge_type outer \ --plink ~/bin/plink \ --out out/ex_outer \ --set_missing_to_reference \ --output_type vcf
The help message output is pasted below for convenience:
usage: bedmerger.py [-h] [--bed [BED [BED ...]]] [--vcf [VCF [VCF ...]]]
[--out OUT] [--output_type {bed,vcf}]
[--merge_type {inner,outer,left,right}]
[--retained_snp RETAINED_SNP]
[--keep_snp_id {left,false,merge}] [--pwd PWD] [--twd TWD]
[--check_reference] [--reference_path REFERENCE_PATH]
[--dropped_snp DROPPED_SNP] [--set_missing_to_reference]
[--chromosomes [CHROMOSOMES [CHROMOSOMES ...]]]
[--plink PLINK] [--logfile LOGFILE] [-d] [-v]
A python wrapper around plink 1.9 for merging data sets in various file
formats. Assumptions (currently NOT checked): - same positions implies same
variant - indels are removed - alleles given on same strand in all files
optional arguments:
-h, --help show this help message and exit
--bed [BED [BED ...]], --bedfiles [BED [BED ...]]
The bedfiles to merge. The bim and fam files are
assumed to have the same name
--vcf [VCF [VCF ...]], --vcffiles [VCF [VCF ...]]
The files in vcf format to merge
--out OUT the output file name prefix. Will have ending
bed/bim/fam (for bed)or vcf.gz (for vcf output)
--output_type {bed,vcf}
the format of the output file
--merge_type {inner,outer,left,right}
how the SNP are merged. Default is an outer join,
keeping all SNP. `inner` only keeps SNP that are
shared between populations. `left` and `right` keep
all SNP from the first/second data set, respectively
in each merge.
--retained_snp RETAINED_SNP
file name of the file with all snp included in the
analyssis
--keep_snp_id {left,false,merge}
if SNP id's should be retained. `false` will set it to
chr_pos_a1_a2, left keeps the id from the leftmost
file, as long as it is not na. `merge` concatenates
the SNP ids.
--pwd PWD, --working-directory PWD
The working directory for relative paths
--twd TWD, --temp-directory TWD
The directory where temporary files are stored.
created if it does not exist
--check_reference, --check-reference
should SNP alleles be checked against reference
sequence?
--reference_path REFERENCE_PATH, --reference-path REFERENCE_PATH
A folder with the reference sequence files in fasta
format, only required when --check_reference is used.
hg18, hg19, ancestral_hg19 and ancestral_hg38 lead to
reference sequences and ancestral sequences for these
genomes, respectively.
--dropped_snp DROPPED_SNP
File with all SNP that were dropped from the analysis
--set_missing_to_reference
should SNP absent from a data set be called as
reference?
--chromosomes [CHROMOSOMES [CHROMOSOMES ...]], --chromosome [CHROMOSOMES [CHROMOSOMES ...]]
list of chromosomes to be included in data
--plink PLINK path to the plink executable to be used
--logfile LOGFILE file name for log file, default is stdout
-d, --debug Print lots of debugging statements
-v, --verbose Be verbose