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PhredUtils conversion to log probabilities has insufficient resolution for PLs #1569

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fnothaft opened this Issue Jun 16, 2017 · 1 comment

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fnothaft commented Jun 16, 2017

Genotype Phred Likelihoods aren't restricted to <256, as Phred scores are typically restricted for reads. As such, we clip when dealing with large PLs, e.g.,:

chr22	18030096	.	TAAA	T,TA,TAA,<NON_REF>	564.73	.	BaseQRankSum=-0.133;ClippingRankSum=-1.438;DP=114;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQ=69.72;MQ0=0;MQRankSum=-0.686;ReadPosRankSum=-0.013	GT:AD:DP:GQ:PL	2/3:13,3,17,17,0:50:86:602,508,1628,86,678,553,137,342,0,281,467,744,353,309,659

@fnothaft fnothaft added the bug label Jun 16, 2017

@fnothaft fnothaft self-assigned this Jun 16, 2017

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fnothaft Jun 16, 2017

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See further discussion of accuracy for converting log (p - 1) to log p here.

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fnothaft commented Jun 16, 2017

See further discussion of accuracy for converting log (p - 1) to log p here.

@fnothaft fnothaft added this to the 0.23.0 milestone Jun 16, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Jun 19, 2017

[ADAM-1569] Support log space probabilities in PhredUtils for extreme…
…ly high Phred scores.

Resolves bigdatagenomics#1569. Can support phred scores >1,000.

fnothaft added a commit to fnothaft/adam that referenced this issue Jun 19, 2017

[ADAM-1569] Support log space probabilities in PhredUtils for extreme…
…ly high Phred scores.

Resolves bigdatagenomics#1569. Can support phred scores >1,000.

fnothaft added a commit to fnothaft/adam that referenced this issue Jun 19, 2017

[ADAM-1569] Support log space probabilities in PhredUtils for extreme…
…ly high Phred scores.

Resolves bigdatagenomics#1569. Can support phred scores >1,000.

fnothaft added a commit to fnothaft/adam that referenced this issue Jun 22, 2017

[ADAM-1569] Support log space probabilities in PhredUtils for extreme…
…ly high Phred scores.

Resolves bigdatagenomics#1569. Can support phred scores >1,000.

@heuermh heuermh closed this in 7913e76 Jun 22, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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