anazhmetdin/chimaera

parsing SAM files to extract chimeric alignments and report each chimeric locus with its supporting reads

Chimeara

description

This is a chimeric alignment reporter. Chimeric alligments correspond to some structural variation in the sequenced sample in comparison to the reference genome.

The main element in this tool is the locus. A locus is defined by three properties:

• Chromosome
• Position
• Direction (0 for forward direction, 1 for reverse direction)

Therefor, this tool reports all reads that covers two distinct loci such as following:

Dependencies:

• Samtools
• gperf
• g++

Input

• SAM file of the mapped sample
  • You will be prompted to either use the same hash function or to create a new one. You are supposed to create new hash function for different samples
  • Then, you will be prompted to enter the maximum allowed gap between reads to be considered on the same locus
  • Finally, you will be prompted to enter the the minimum number of supporting reads for each locus to be reported

Output

• One text file named supported_loci.txt in the pipline_run directory following this template for each loci:

@$num_supporting_reads $pos_1st_locus-$end_pos_1st_locus $pos_2nd_locus-$end_pos_2nd_locus

>>$1st_reference_name $1st_locus_direction

>>$2nd_reference_name $2nd_locus_direction

$read_line_supporting_1st_locus

$read_line_supporting_2nd_locus

$read_line_supporting_1st_locus

$read_line_supporting_2nd_locus

$read_line_supporting_1st_locus

$read_line_supporting_2nd_locus

To run this pipeline use this line on a Linux terminal:

./pipeline_supported_chim_loci.sh $SAM_file_name.sam