6.8 polymorphicWindows
Identifying windows for which samples are polymorphic
polymorphicWindows is used to identify polymorphic sites in the samples.
6.8.1 Input
Required inputs :
--vcf Input_VCF_file.vcf.gz |
Input VCF file. |
Optional inputs :
None
Specific Parameters :
--limitLines integer_value |
To limit amount of lines to be read from VCF file. Default = Will parse entire VCF. |
--regions \*.bed |
To limit analysis to regions defined in BED file. Default = Will parse entire VCF. |
--filterDepth integer_value,integer_value |
To keep only the samples with indicated sample depth (inclusive). Default = Will keep all sites regardless of depth. |
--maxMissing numeric_value |
To filter out sites which has more than the indicated data fraction missing. numeric_value must be between 0 and 1 (inclusive). Default = keep sites regardless of missingness. |
--minMAF numeric_value |
To keep only sites for which minor allele frequency is at the least the indicated number. Default = all sites are kept regardless of minor allele frequency. |
--minVarQual numeric_value |
To only store sites with minimum variant quality as indicated or more. Default = Will keep sites regardless of their variant quality. |
--chr or '--limitChr' |
To keep only specified chromosomes. Default = Will keep all chromosomes. |
- 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.
6.8.3 Usage Example
#! /bin/bash
. $(dirname $0)/find_atlas
. $(dirname $0)/simulate_vcf --sampleSize 11 --fixedSeed 181
echo "chr1 1000 10000" > bed.bed
echo "chr2 2 3" >> bed.bed
echo "chr3 0 10" >> bed.bed
echo "chr3 100 110" >> bed.bed
echo "chr3 200 210" >> bed.bed
echo "chr3 300 310" >> bed.bed
echo "chr3 400 410" >> bed.bed
echo "chr3 500 510" >> bed.bed
out="polymorphicWindows"
$atlas --task polymorphicWindows --vcf simulate.vcf.gz --regions bed.bed \
--fixedSeed 183 --out $out --logFile $out.out 2> $out.eout