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Mapping of ISGC SNP chip probes

posted on 02.07.2019, 01:07 authored by Rudiger BrauningRudiger Brauning
Probe sequences were taken from the Illumina manifests and mapped onto the Rambouillet genome (GCA_002742125.1) using bwa mem v0.7.17-r1188 with default settings (Indels were ignored)
For each SNP a probe pair was constructed by using AlleleA_ProbeSeq and appending either the reference or the alternative allele.
Only probe pairs where accepted that passed following filters.
-both probes are mapped
-one probe is mapped with 0 mismatches
-both probes are not multi-mapped
-no indels were allowed
-both probes had to map in the same orientation
-both probes had to map to the same position
-mapped probes had between them exactly 1 mismatch, the SNP.

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