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ANGSD / angsd

Program for analysing NGS data.
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bcf output file with "." at QUAL column #630

Open martaolmu opened 3 months ago

martaolmu commented 3 months ago

Hi! I'm trying to obtain a bcf using this command:

$pth_angsd/angsd \
    -GL 2 \
    -out $pth_o/$o_name \
    -rf $bedfile \
    -nThreads $threads \
    -snp_pval 1e-6 \
    -doPost 1 \
    -doMaf 1 \
    -doMajorMinor 5 \
    -dobcf 1 \
    -doGeno 1 \
    -anc $pth_anc \
    -ref $ref \
    -C 50 \
    -baq 1 \
    -minMapQ 20 \
    -minQ 20 \
    -uniqueOnly 1 \
    -remove_bads 1 \
    -only_proper_pairs 1 \
    -skipTriallelic 1 \
    -bam $pth_i/$i_name

For some reason, the bcf file that I obtain has all the values of the QUAL column coded as "." Additionally, in case it helps, when I convert the bcf to vcf using this command: $pth_bcftools/bcftools view $pth_i/$i_name_prefix.bcf | $pth_bcf/vcfutils.pl varFilter -D92 > $pth_o/$o_name_prefix.flt.vcf

The vcf that I obtain is somehow incorrectly formatted (the scaffold should be named "Scaffold_3" without these 0-1 or .-1 that they appear in the beggining. Moreover the first QUAL value is zero and the next ones are still "." ). Here's a little piece of the vcf :

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  first.bed
0-1Scaffold_3    178     .       G       A       0       PASS    NS=12;AF=0.157716       GT:GL:PL:GP     0/0:0,-1.20357,-15.5068:0,12,155:0.977101,0.02
.-1Scaffold_3    192     .       A       T       .       PASS    NS=12;AF=0.056698       GT:GL:PL:GP     0/0:0,-0.602002,-8.35407:0,6,84:0.97082,0.0291
.-1Scaffold_3    212     .       T       C       .       PASS    NS=12;AF=0.0925391      GT:GL:PL:GP     0/0:0,-1.204,-16.7081:0,12,167:0.98741,0.01258

Any ideas on how to fix this? I guess it is something format related but I've been looking into this for weeks and I cannot find a solution.

Many thanks!

Marta

martaolmu commented 2 months ago

Hi!

Just in case it is useful for somebody, I think this is caused by the angsd version I was using. I was using the last one (0.940) and when I switched to the 0.934 the issue was solved. I have only used these versions but maybe others work too.

Marta