Variant Analysis

Usage -i rnaseq.bam -f reference.fa -F reference.2bit -o BlatCorrection -V -T



-i      BAM file

-I      Sort input BAM file

-f      Genomic fasta file

-F      Genomic fasta file in 2bit format for gfServer

-t      Num. of working threads [1]

-o      Output Folder [BlatCorrection_XXXX]

-k      List of chromosomes to skip separated by comma or file

-r      Regions in GFF in which Blat will be launched

-s      Sort GFF (if unsorted). It requires grep and sort unix executables.

-q      Minimum quality score [25]

-Q      Fastq offset value [33]

-V      Verify if gfServer is alive

-T      Stop gfServer at script end

-h      Print the help

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