Changes

Steps:

Steps:

# Run this program and pipe it into samtools sort by query name

# Run this program and pipe it into samtools sort by query name

#* <pre>./bam filter --in <your InputFile> --refFile <your reference file> --out -.bam <any other options> | samtools sort -n - temp.bam</pre>

#* <pre>./bam filter --in <your InputFile> --refFile <your reference file> --out -.bam <any other options> | samtools sort -n - tempQuerySort</pre>

# Run samtools fixmate and pipe it into samtools sort by position

# Run samtools fixmate and pipe it into samtools sort by position

#* <pre></pre>

#* <pre> samtools fixmate tempQuerySort.bam - | samtools sort - finalResult</pre>

 

 

=== Parameters ===

=== Parameters ===

Input Parameters

Input Parameters

  --in [testFiles/testFilter.sam], --out [-],

  --in [../../originalBamFile.bam],

--refFile [testFiles/chr1_partial.fa], --noeof, --qualityThreshold [30],

--out [-.bam], --refFile [/home/mktrost/data/human.g1k.v37.fa], --noeof,

--defaultQualityInt [20], --mismatchThreshold [0.49]

--qualityThreshold [60], --defaultQualityInt [20], --mismatchThreshold [0.10]

open and prefetch reference genome testFiles/chr1_partial.fa: done.

open and prefetch reference genome /home/mktrost/data/human.g1k.v37.fa: done.

Number of Reads Clipped by Filtering: 8

Number of Reads Clipped by Filtering: 704578

Number of Reads Filtered Due to MismatchThreshold: 1

Number of Reads Filtered Due to MismatchThreshold: 0

Number of Reads Filtered Due to QualityThreshold: 2

Number of Reads Filtered Due to QualityThreshold: 13064

</pre>

</pre>