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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
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bam file for dng-phaser #311

Closed mariliascliar closed 4 years ago

mariliascliar commented 4 years ago

Hi, I´m trying to run dng-phaser but it seems it is not reading the bam file at all. When I include the --bam flag, dng-phaser return the result below. Independent if I specify the pathway for bam file or not, the result is the same. When I don´t include the --bam flag, it return an error "INPUT ERROR! Please specify the list of DNMs, list of Parental GTs and the BAM file!"

Do you have any suggestion to resolve this issue? Thank you!

dng-phaser --dnm dnm_file.txt --pgt ind1.PGT.txt --bam ind1.bam --window 300 DeNovoGear v1.1.1-unknown --- SNV Phaser

List of DNMs: dnm_file.txt, List of parental GTs: ind1.PGT.txt

DNM_pos chr1:32091818 INHERITED C VARIANT T - Insufficient reads present to phase this site. DNM_pos chr12:52772135 INHERITED G VARIANT A - Insufficient reads present to phase this site. The number of lines read DNM file is 2

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reedacartwright commented 4 years ago

dng-phaser is not supported any more. I recommend that you try whatshap https://whatshap.readthedocs.io/en/latest/guide.html instead of phaser.