Software for painlessly estimating average nucleotide diversity within and between populations
115
stars
14
forks
source link
version 1.2.11.beta1., pixy: error: unrecognized arguments: --variant_filter_expression DP -invariant_filter_expression DP #113
Open
AliBasuony2022 opened 1 month ago
Dear friends,
I have got the below error with pixy, version 1.2.11.beta1.
"pixy: error: unrecognized argumentusage: pixy [-h] --stats {pi,dxy,fst} [{pi,dxy,fst} ...] --vcf [VCF] --populations [POPULATIONS] [--window_size [WINDOW_SIZE]] [--bed_file [BED_FILE]] [--n_cores [N_CORES]] [--output_folder [OUTPUT_FOLDER]] [--output_prefix [OUTPUT_PREFIX]] [--chromosomes [CHROMOSOMES]] [--interval_start [INTERVAL_START]] [--interval_end [INTERVAL_END]] [--sites_file [SITES_FILE]] [--chunk_size [CHUNK_SIZE]] [--fst_type {wc,hudson}] [--bypass_invariant_check {yes,no}] [--version] [--citation] [--silent] pixy: error: unrecognized arguments: --variant_filter_expression DP -invariant_filter_expression DP
Running comand
pixy --stats pi fst dxy \ --vcf samples12Ali_chr1_autosomes_allsites_filtered.vcf.gz \ --populations samples12Ali_sampleIDs_popfile.txt \ --window_size 10000 \ --interval_start 107000000 \ --interval_end 107300000 \ --variant_filter_expression DP>=10,GQ>=20,RGQ>=20 \ -invariant_filter_expression DP>=10,RGQ>=20 \
Are these arguments not avilable for this version?
Kind regrads, Ali