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Minor fix on line 72 #6

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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -10,7 +10,7 @@ Please open a new "issue" on github or contact authors Akdes.Harmanci@uth.tmc.ed

# Installation

Type make to build BAFExtract. The executable is built under bin directory. The code is tested on various Unix based systems.
Type make to build BAFExtract. The executable is built under `bin` directory. The code is tested on various Unix based systems.

# Usage

Expand Down Expand Up @@ -69,4 +69,4 @@ fetchChromSizes hg19 > hg19.list
```{bash}
mkdir test; samtools view SRR1295366.sorted.bam | ./bin/BAFExtract -generate_compressed_pileup_per_SAM stdin hg38.list test 50 0; ./bin/BAFExtract -get_SNVs_per_pileup hg38.list test ./hg38/ 20 4 0.1 test.snp
```
Note: In the example above ./BAFExtract -generate_compressed_pileup_per_SAM uses mimunum mapping quality threshold 50. Depending on the aligner you used the MAPQ-Values can differ a lot and the setting of [Minimum mapping quality] to 50 could mean that no reads are surviving the filtering, only due to the aligners implementation of MAPQ. (acknowledgements to Tobias Tekath)
Note: In the example above ./BAFExtract -generate_compressed_pileup_per_SAM uses mininum mapping quality threshold 50. Depending on the aligner you used the MAPQ-Values can differ a lot and the setting of [Minimum mapping quality] to 50 could mean that no reads are surviving the filtering, only due to the aligners implementation of MAPQ. (acknowledgements to Tobias Tekath)