snps.vcf files without snp information

[tthye1]

Hi,

when running nullarbor the raw snps.raw.vcf files were not converted correctly to the snp.vcf files.

Any help?

Best,

Thorsten

[17:38:23] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5

options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [n] no fail on reference inconsistency for non SNPs false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa

[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?) [variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: NC_008611.1:186529-186531 # @ nullarbor.log

[tthye1]

The error occurred when putting nullarbor in a conda environment (env). A new installation of nullarbor, as recommended, resolved the error.