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version 1.2.11.beta1., pixy: error: unrecognized arguments: --variant_filter_expression DP -invariant_filter_expression DP #113

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AliBasuony2022 opened this issue Jul 13, 2024 · 0 comments
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@AliBasuony2022
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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

@AliBasuony2022 AliBasuony2022 added the help wanted Extra attention is needed label Jul 13, 2024
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