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jpuritz / dDocent

a bash pipeline for RAD sequencing
ddocent.com
MIT License
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Discrepancy between dDocent_filters.sh and SNP Filtering Tutorial #35

Closed SheaML closed 7 years ago

SheaML commented 7 years ago

Several of the filters (allele balance, mapping quality, quality/depth) contained in dDocent_filters.sh are not run with the same parameters as the step-by-step examples in the SNP filtering tutorial. Here's the relevant line (17) in dDocent_filters.sh:

vcffilter -s -f "AB > 0.2 & AB < 0.8 | AB < 0.01 | AB > 0.99" -s -g "QR > 0 | QA > 0 " $1 | vcffilter -s -f "QUAL / DP > 0.2" | vcffilter -s -f "MQM / MQMR > 0.25 & MQM / MQMR < 1.75" > $2

And the respective parameters from the step-by-step tutorial:

AB > 0.25 & AB < 0.75 | AB < 0.01 MQM / MQMR > 0.9 & MQM / MQMR < 1.05 QUAL / DP > 0.25

jpuritz commented 7 years ago

The dDocent_filters script represents my most up-to-date filters. The tutorial is only supposed to teach principles and philosophy.

I recommend everyone take the time to optimize these parameters for their own data.