6.3 ancestralAlleles

Writing FASTA-file with ancestral alleles

6.3.1 Input

Required inputs :

--alleleCounts Input_file_alleleCounts.txt.gz	A zipped text file containing the MLE allele counts for all positions and populations.
--fastaIndex Reference_fasta_file.fasta.fai	Index file for the reference genome file.

Optional inputs :

• None

Specific Parameters :

--minorCountMaximum integer_value	To set the maximum count of minor allele. Default = the maximum count of minor allele is set to 0.
--totalCountMinimum integer_value	To set the minimum total allele count. Default = minimum total allele count is set to 0.
--population	.

• See Filter parameters to apply specific filters for bases, reads and parsing window setting.

Engine parameters that are common to all tasks can be found here.

6.3.2 Output

*_ancestralAlleles.fasta.fasta	A fasta file containing ancestral alleles.
*_ancestralAlleles.fasta.fasta.fai	Index file for the fasta file containing ancestral alleles.

6.3.3 Usage Example

#! /bin/bash

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate_vcf --fixedSeed 28

out="alleleCounts"
$atlas --task alleleCounts --vcf simulate.vcf.gz --outFormat withAlleles \
       --fixedSeed 27 --out $out --logFile $out.out 2> $out.eout

out="ancestralAlleles"
$atlas --task ancestralAlleles --alleleCounts alleleCounts_alleleCounts.txt.gz \
       --fastaIndex simulate.fasta.fai \
       --minorCountMaximum 2 --totalCountMinimum 4 \
       --fixedSeed 26 --out $out --logFile $out.out 2> $out.eout