mgalardini
commented
1 month ago Hi, could you be more specific with the errors you are seeing please?
Open akarkaba opened 1 month ago
mgalardini
commented
1 month ago Hi, could you be more specific with the errors you are seeing please?
The out put of snps.vcf of nullabor pipeline is within directory of each file, however the output is of such
bcftools_viewCommand=view --include '(GT="1/1" || GT="1|1") && INFO/DP>=0 && AF>=0' snps.raw.vcf; Date=Tue Oct 24 23:32:02 2023
bcftools_annotateVersion=1.9+htslib-1.9
bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AF,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Tue Oct 24 23:32:02 2023
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT snippy
NC_002953.3 987 . G T 8046.03 . AF=1;AO=230;DP=231;QA=9019;QR=22;RO=1;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:231:1:22:230:9019:-808.974,-67.338,0
When merging several files to run the following pyseer --phenotypes resistances.pheno --vcf snps.vcf.gz --load-m mash_mds.pkl --lineage --print-samples > penicillin_SNPs.txt
Errors appearing I think its either with the merging or pyseer not happy with the current format?