Methods

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Alignment

Sequences were aligned to WS245 using BWA (version 0.7.8-r455). Optical/PCR duplicates were marked with PICARD (version 1.111).

Variant Calling

SNV calling was performed using bcftools (version 1.3).

Filtering

Sites with greater than 10% missing or greater than 90% heterozygous calls across all isotypes were removed. Individual calls with the following parameters were removed:

  • Depth of coverage (DP) <= 10
  • Quality (QUAL) < 30
  • Mapping Quality (MQ) < 40. Only applied to ALT calls.
  • Number of high-quality non-reference bases (DV) / Depth of Coverage (DP) < 0.5. Applied only to ALT calls.

Annotation

Variants were annotated using SnpEff (version 4.1g) using the WS241 database.




1.1.1