Hi
I'm currently trying to use a Singularity image of GLnexus to merge the GATK sample.chr4.vcf.gz files for chromosome 4 only.
I using the following command and get error:
{orig_names: [MIN_DP, DP], name: DP, description: "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}
{orig_names: [AD], name: AD, description: "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">", type: int, number: alleles, default_type: zero, count: 0, combi_method: min, ignore_non_variants: false}
{orig_names: [SB], name: SB, description: "##FORMAT=<ID=SB,Number=4,Type=Integer,Description=\"Per-sample component statistics which comprise the Fishers Exact Test to detect strand bias.\">", type: int, number: basic, default_type: missing, count: 4, combi_method: missing, ignore_non_variants: false}
Hi I'm currently trying to use a Singularity image of GLnexus to merge the GATK sample.chr4.vcf.gz files for chromosome 4 only. I using the following command and get error:
$ singularity run --bind /work/WFS/09.tmp:/home/wufusheng/04.tmp_bamfile /home/Singusoft/glnexus.sif glnexus_cli --config gatk --list chr4.list --dir chr4.GLnexus.DB --mem-gbytes 170 >chr4.bcf [204941] [2023-12-19 15:46:35.312] [GLnexus] [info] glnexus_cli release v1.4.3-0-gcecf42e Sep 20 2021 [204941] [2023-12-19 15:46:35.314] [GLnexus] [info] detected jemalloc 5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756 [204941] [2023-12-19 15:46:35.317] [GLnexus] [info] Loading config preset gatk [204941] [2023-12-19 15:46:35.325] [GLnexus] [info] config: unifier_config: drop_filtered: false min_allele_copy_number: 1 min_AQ1: 70 min_AQ2: 40 min_GQ: 40 max_alleles_per_site: 32 monoallelic_sites_for_lost_alleles: true preference: common genotyper_config: revise_genotypes: true min_assumed_allele_frequency: 9.99999975e-05 snv_prior_calibration: 1 indel_prior_calibration: 1 required_dp: 1 allow_partial_data: false allele_dp_format: AD ref_dp_format: MIN_DP output_residuals: false more_PL: false squeeze: false trim_uncalled_alleles: false top_two_half_calls: false output_format: BCF liftover_fields:
Does anyone know how to resolve the issues?