I was trying to left normalize my vcf file using following command:
bcftools norm -f reference.fasta -m -any input.vcf > output.norm.vcf
However this gives the following error:
Non-ACGTN alternate allele at 1:278165 .. VCF:'-3AGG'
It looks like the variant caller returned all deletions and insertions like this:
1 5387285 . C +2TG 1 5387316 . G -8TGTGTATC
This file format was produced by SCCaller 2.0.0, there are several unconventional output fields produced by this caller but but the repository isn't maintained.
Is this an issue of the vcf format or does this means that there is a non-ACGTN character on position 1:278165 in the fasta reference file? I don't see anyting out of the ordinary at this position using IGV.
What would be the best way forward? I tried the following command to extract non-ACGTN allels but it outputs all alleles:
bcftools view -i 'ALT !~ "^[ACGTN]+$"' input.vcf.gz > errors.vcf
EDIT: including several lines of vcf file
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 1 89946 . A T 68 . NS=1 GT:SO:AD:BI:GQ:PL 0/1:False:3,18:0.973:68:273,164,49,117 1 286158 . A +2TG 78 . NS=1 GT:SO:AD:BI:GQ:PL 0/0:NA:11,10:0.982:78:154,97,175,456 1 900119 . A G 150 . NS=1 GT:SO:AD:BI:GQ:PL 0/0:False:17,14:0.995:150:214,136,321,657 1 932613 . G -4TTTC 62 . NS=1 GT:SO:AD:BI:GQ:PL 0/1:NA:4,18:0.998:62:274,165,103,173 1 1168310 . T +2CA 35 . NS=1 GT:SO:AD:BI:GQ:PL 0/0:NA:18,5:0.985:35:77,55,91,712```