Rock ptarmigan autosomal consensus sequence

Rock ptarmigan autosomal consensus sequence used as input for PSMC. The file was generated from a filtered bam file using the samtools mpileup, bcftools and vcfutils.pl (vcf2fq) pipeline (downgrading mapping quality for reads containing excessive mismatches (-C) to 50, minimum read depth (-d) set to...

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Bibliographic Details
Main Authors: Kozma, Radoslav, Melsted, Páll, Magnússon, Kristinn P., Höglund, Jacob
Format: Dataset
Language:unknown
Published: 2015
Subjects:
Effective population size
Climate hange
PSMC
rock ptarmigan
Online Access:http://hdl.handle.net/10255/dryad.102417
https://doi.org/10.5061/dryad.11p3v/2
Description
Summary:Rock ptarmigan autosomal consensus sequence used as input for PSMC. The file was generated from a filtered bam file using the samtools mpileup, bcftools and vcfutils.pl (vcf2fq) pipeline (downgrading mapping quality for reads containing excessive mismatches (-C) to 50, minimum read depth (-d) set to 1/3 of the mean genome coverage (33) and maximum read depth (-D) set to twice the mean genome coverage (202)). All non-autosomal sites were discarded.

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