User: dario.galanti92
dario.galanti92 • 0
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Posts by dario.galanti92
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... Yes, that was indeed wrong, apologies. I fixed it now. ...
written 5 weeks ago by
dario.galanti92 • 0
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... Here is a quick way to count **biallelic** SNPs in vcf.gz files (use "cat" instead of "zcat" for uncompressed vcf files):
zcat input.vcf.gz | awk '{if ($4~/^[ACGT]$/ && $5~/^[ACGT]$/){c++}} END {print c}'
...
written 5 weeks ago by
dario.galanti92 • 0
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... Solved it! I removed all scaffolds harbouring less than 3 SNP in my vcf file and it worked smoothly! Good luck to anyone else having the same problem! ...
written 10 months ago by
dario.galanti92 • 0
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... I have a multisample vcf file from a study species with a pretty fragmented reference genome. I already applied the basic filtering steps to my vcf using vcftools.
1- Sample filtering: filter out low coverage samples
2- Site and genotype filtering with the following vcftools parameters: --minDP 3 -- ...
written 10 months ago by
dario.galanti92 • 0
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