merged snps files

[akarkaba]

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?

[mgalardini]

Hi, could you be more specific with the errors you are seeing please?