STACKS output VCF file,, --site-quality result value is -1?

[shazia kunvar]

Hi Julien and Stacks Community,

I have used ref_map.pl program, then I have used population program to get vcf file as an output. 

I am showing results and commands that I have used. 

ref_map.pl version 2.41 started at 2020-08-20 17:17:39

/usr/local/bin/ref_map.pl -T 8 -o ./Ref_Aligned_256_stacks_1_pop_rmpcrduplicate_r_0.80/ --popmap ./scan_popmap_ref_256_1.tsv --samples ./Ref_Aligned_256_bosTau8_BWA_0.7.17/ --rm-pcr-duplicates -X populations: --min-samples-per-pop 0.80

zgrep -c "^>" catalog.fa.gz 

6417724

populations v2.41, executed 2021-01-01 08:50:53 (zlib-1.2.11)

populations -P . --popmap scan_popmap_ref_256_1.tsv --vcf -t 8 -O ../Ref_Aligned_256_bosTau8_1_pop_rmpcrduplicate_r_0.80/bostau8_rmpcr_population_vcf_filtered_30_Dec_2020_r_0_80/ -r 0.80

Locus/sample distributions will be written to '../Ref_Aligned_256_bosTau8_1_pop_rmpcrduplicate_r_0.80/bostau8_rmpcr_population_vcf_filtered_30_Dec_2020_r_0_80/populations.log.distribs'.

populations parameters selected:

  Percent samples limit per population: 0.8

  Locus Population limit: 1

  Percent samples overall: 0

  Minor allele frequency cutoff: 0

  Maximum observed heterozygosity cutoff: 1

  Applying Fst correction: none.

  Pi/Fis kernel smoothing: off

  Fstats kernel smoothing: off

  Bootstrap resampling: off

 (i) grep -v "^#" populations.snps.vcf | wc -l 

2452

 (ii)grep -v "^#" populations.sumstats.tsv | wc -l 

2452

(ii) grep -v "^#" populations.haps.vcf | wc -l 

1183

 (iv) grep -v "^#" populations.hapstats.tsv | wc -l 

1779

(v) grep -v "^#" populations.haplotypes.tsv | wc -l 

2036

(vi) grep -v "^#" populations.markers.tsv | wc -l 

2036

My  question is ,why I  am getting -1 value for  --site-quality ?

I wanted to calculate --site-quality to filter minQ on vcf. When I calculated --site-quality ,I am getting -1 value for all the samples showing in the last. I do not know why I  am getting -1 value. 

vcftools --vcf populations.snps.vcf --site-quality --out  populations.snp_site_quality

awk '{ print $3 }'  populations.snp_site_quality.lqual | sort -n | uniq -c

   2452 -1

      1 QUAL

Output file populations.snp_site_quality.lqual  looks like this given below.

CHROM POS QUAL

chr10 280106 -1

chr10 10242269 -1

chr10 16907941 -1

chr10 16908045 -1

chr10 16908074 -1

chr10 16907961 -1

chr10 70983309 -1

chr10 87198817 -1

It would be really appreciable if anyone of you could guide me or give me an idea that  what could be the reason behind this?

Thank you so much in advance.