outLyzer V3.2

Add GT annotation in vcf to be fully compatible with annotation tools (Annovar)

outLyzer V3.1

This version is compatible with BAM files containing UMI data (update on "N" bases management). UMI deduplication and read correction has to be done before analysis.

runs with python 3.10

Full Changelog: v2...3.1

outLyzer V3

Suppression:

• low coverage detection: replaced with "-force" option

Ameliorations:

• outLyzer V3 works with python 3.0 version and has been tested with samtools 1.9.
• "force" option: This option replace and overrides "low coverage detection" function and has been specially created for samples with low noise background (lymphocytic DNA for the detection of mosaic mutations / ctDNA). On this kind of samples, noise background determination can be biased due to lack of alternative reads in the region close to the mutation. In such a case, this option force noise background determination to drop below a determined threshold (a proportion of observed depth at mutation position) by continuing iterations in thompson-Tau test until the defined threshold is reached. If this option is triggered during the evaluation of a mutation, this will be flagged by a "*" on the OUTLIER value in vcf file.

ex:
chr4 55602765 . G C 27.35 PASS DP=786;AF=4.326;SDQ=2.63;OUTLIER=3* BAL:WTbal:MSS 17/17:366/386:S5d11

If OUTLIER=NA, the force option has been triggered but no value could be determined.

outLyzer v2

Release note outLyzer v.2 (31/05/2018) :

Corrections:

• -samtools option is now taken into account and the indicated path used to launch samtools

ameliorations:

• FRcor option: with this option, the alternative Forward / Reverse Balance is corrected based on wild-type Forward /Reverse balance.
• MSS data in vcf: for each variant reported in vcf file, a sequence analysis is realized to search for stretchs (repetition of the same nucleotide) or repeated motifs nearby the mutation.
  This could be in some cases an indication of a false positive induced by an alignment issue
  MSS output: - None ==> no stretch or repeated motif around mutation
  - S10d1 ==> stretch of 10 nucleotide located 1 base away from mutation
  - M12d6 ==> repeated motif with a total length of 12 bases located 6 bases away from mutation
• low coverage detection: if less than 10% of genomic positions in the window of analysis (200 bp around position to test by default) contain alternative reads, the algorithm can't estimate an accurate noise background.
  This condition is generally observed for low coverage regions (ex: 30x exome). In this case, the noise background is fixed by default to 5% of sequencing depth at the considered position.
• uncoveredRegions report: In all the genomic regions to analyse (specified in input bed file), if some regions are not covered (sequencing depth = 0), these are reported in output as a specific bed file