DonFreed

#!/usr/bin/env snakemake

# Requires Python3.6 or greater

rule align_A:
  output:
    outfile = "align__A/{sample}.bam"
  shell:
    '''
    mkdir -p $(dirname {output.outfile})

DonFreed

Creating a gVCF file for all samples in the 1000 Genomes project

Table of Contents

• Introduction
• Requirements
• Setup
• Installing Python
• Installing StarCluster
• Configuring StarCluster
• Setting up a VPC

DonFreed

63	63
49	66
211	27
56	64
140	18
65	65
68	61
39	30
75	58
10	18

DonFreed

def find_pl_allele(allele, n_alleles, ploidy):
    gts = [0] * ploidy
    idx = ploidy - 1
    pl_pos = 0
    while (sum(gts) <= ploidy * (n_alleles - 1)):
        if allele in gts:
            yield pl_pos
        if sum(gts) == ploidy * (n_alleles - 1):
            break