poisonalien / basecounts Goto Github PK

git clone https://github.com/PoisonAlien/basecounts
cd basecounts
make

$ basecounts
-------------------------------------------------------------------------
basecounts: A tool to extract nucleotide counts
            of genomic loci from the BAM file. Version: 0.1.0
USAGE:
    basecounts [OPTIONS] <loci> <bam>
    e.g; basecounts target_loci.tsv Tumor.bam
OPTIONS:
    -f  Indexed fasta file. If provided, extracts and adds reference base to the ouput tsv
    -q  Min. mapping quality threshold. Default 10 [Read filter]
    -F  Exclude reads with FLAGS >= INT. Default 3852 [Read filter]
    -o  Output file basename. Default parses from basename of BAM file
ARGS:
    <loci>   loci file (chr\tpos)
    <bam>    Indexed BAM file
OUPUT:
    <output>.tsv    TSV file with nucletide counts for all variants
-------------------------------------------------------------------------

$ head loci.tsv
1	6304615
1	10407830
1	46269731
1	47133825
1	50884996
1	84662414
1	152328587
1	216019313
1	226252155

#basic usage
$ basecounts loci.tsv tumor.bam 

#providing fasta file will add the reference base at the loci
$ basecounts -f GRCh37.fa loci.tsv tumor.bam 

#Output is a TSV file with readcounts suporting all 4 nucleotide bases and INDELS
$ head tumor.tsv 
loci    fa_ref  A       T       G       C       Ins     Del
1:6304615       A       70      0       0       19      0       0
1:10407830      C       0       0       39      50      0       0
1:46269731      A       50      3       1       21      0       0
1:47133825      T       3       37      14      4       0       0
1:50884996      A       51      0       0       15      0       0
1:84662414      G       0       2       81      0       0       0
1:152328587     A       85      3       0       0       0       0
1:216019313     T       0       53      17      0       0       0
1:226252155     G       0       41      52      0       0       0