calling

This module handles everything about the SNV calling.

calling.filterAS_StrandOddsRatio(sras)

Calculates the AS_StrandOddsRatio value for each read using bcftools mpileup.

It runs mpileup for each run BAM file. The resulting files’ names end with .mpileup.vcf, which are saved in the 4-snvCalling/depths directory. Then, these files are processed and filtered, so that only the SNVs positions that pass the filter remain. These results are saved in files whose name end with _filtered.csv, and are saved at 4-snvCalling/depths.

Args:

sras (list): List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID

calling.runJacusa(sras)

Runs JACUSA.

It runs the calling process for each run BAM file. The resulting files’ names end with .jacusa.vcf, and are found in the 4-snvCalling/calling directory.

Args:

sras (list): List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID

calling.runReditools2(sras)

Runs REDItools2.

It creates an index for each reference genome using samtools faidx and runs the calling process for each run BAM file. The resulting files’ names end with .calling.txt, which are saved in the 4-snvCalling/calling directory. Finally, these files are transformed into VCF files. These files’ names end with .reditools.vcf, which are saved in the 4-snvCalling/calling directory

Args:

sras (list): List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID