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** Generate BAQ adjusted GLF files using the following command
** Generate BAQ adjusted GLF files using the following command
samtools-hybrid view -bh chr1.bam 1:0 | samtools-hybrid calmd -Abr - human.v37.fa 2> /dev/null | samtools-hybrid pileup - -g -f human.v37.fa > chr1.bam.glf
samtools-hybrid view -bh chr1.bam 1:0 | samtools-hybrid calmd -Abr - human.v37.fa 2> /dev/null | samtools-hybrid pileup - -g -f human.v37.fa > chr1.bam.glf
** If you want to clip overlapping reads, you can add clipOverlap command
samtools-hybrid view -bh chr1.bam 1:0 |bam clipOverlap --in -.bam --out -.ubam| samtools-hybrid calmd -Abr - human.v37.fa 2> /dev/null | samtools-hybrid pileup - -g -f human.v37.fa > chr1.bam.glf
* For other functionalities please refer to the [[http://samtools.sourceforge.net/ samtools]] website.
* For other functionalities please refer to the [[http://samtools.sourceforge.net/ samtools]] website.
