xtmgah / allelecounter

Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.

allelecounter

Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP. Runs on Python2.7.x and has the following dependencies: pyvcf, Samtools (1.2+), awk.

#Usage Requires a BAM, VCF, and Reference, produces read counts for each allele at each heterozygous SNP. Output is in the same format as the GATK ASEReadCounterTool for cross compatibility. By default this tool will discard duplicate reads, and only count reads whose mates overlap once. For more flexibility please consider using the GATK tool.

##Arguments

• --vcf - VCF file containing genotype for the sample. Must be gzipped and Tabix indexed. To improve runtime this file should be pre-processed to only include bi-allelic heterozygous SNPs.
• --sample - Name of sample to use in VCF file.
• --bam - BAM file containing reads. Duplicates should be marked, and file must be indexed with Samtools index.
• --ref - Reference sequence in FASTA format.
• --min_cov - Minimum coverage for a SNP before it is included in output. Minimum is 2 becuase samtools will not generate pileups for sites with only 1 read.
• --min_baseq - Minimum base quality at the SNP required for reads to be counted.
• --min_mapq - Mimimum mapping qualityfor reads to be counted. Note that due to limitations with Samtools mpileup the maximum value is 93. Any value higher than 93 will be set to 93.
• --o - Output file name.