interm_file_desc

                Description of Intermediate Files 

This directory has intermediate files and can be deleted after HTML report is 
produced in the 'deliverables' directory.

    .fastq.gz      Filtereed fastq file
    .bam           Alignment bam file	
    .fliter.log    Filtering log
    .bwa.log       BWA alignment log
    .abra.log      ABRA realignment log if realignment is performed.
     <sample>.log  General log for sample processing 
    .chr           Counts of reads mapped on different chromosomes 
    .cnt           Counts of reads at different stages of pre-processing
    .can           File for generating CanvasXpress alignment view
    .hdr           File for generating Homology Directed Repair plot
    .len           Contains read counts for WT and indels of various lengths  
    .pct           Contains summary read stats of WT and indel
    .snp           Contains mutation stats generated by pysamstats around CRISPR site
    .tgt           Contains sequence in sgRNA region in each read spanning
                      this region. Indel start and end locations are indicated.
                      Indel location can extend outside the region. Read ID and 
                      strand are also shown.
    .hdr.bed       Coordinates of HDR region
    .hdr.seq       Similar to .tgt but the sequence region is in HDR region
    .var           Contains mutation stats generated by pysamstats in amplicon
    .done          Signal file generated when processing of a sample succeeds 
    .failed        Signal file generated when processing of a sample fails
    tmp            Directory containing temporary files generated by ABRA.
    <name>.*.txt   Combined data of various type of all samples in a CRISPR site.
    .extendedFrags Merged fastq reads if --merge option is used.
    .notCombined_1 Unmerged fastq reads from R1 if --merge option is used.