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Place gap consistently
By default, blasr places gap in-consistently when aligning a sequence and its reverse complement sequence. To produce alignments with gaps placed consistently for better variant calling, users need to turn on the
--placeGapConsistently (false) Place gaps consistently in alignments of a read as alignments of its reverse complementary sequence.
Here is a toy example,
REF : TTTTTTAAACCCC READ1: TTTTTTACCCC READ2: GGGGTAAAAAA
, where READ1 and READ2 are reverse-complementary to each other.
In below alignments, gaps are placed inconsistently.
REF : TTTTTTAAACCCC READ1 : TTTTTTA--CCCC RevComp(READ2): TTTTTT--ACCCC
In below alignments, gaps are placed consistently (with --placeGapsConsistently turned on).
REF : TTTTTTAAACCCC READ1 : TTTTTTA--CCCC RevComp(READ2): TTTTTTA--CCCC
Why place gap consistently
It's preferred to place gap consistently if users want to call a consensus sequence from multiple alignments or call single nucleotide variants (SNPs), because the output alignments will make it easier for variant callers to call variants.
How to turn on place gap consistently option via CMD blasr
blasr query target --out outfile --placeGapConsistently
How to turn on place gap consistently option via CMD pbalign
pbalign query target outfile --algorithmOptions "--placeGapConsistently"
How to turn on palce gap consistently option via SMRT Link Resequencing pipeline
Data Management Page -> Click
Analyze -> Select
Analysis Application -> Click
Advanced Analysis Parameters -> Identify
Algorithm options Txt Box -> Add " --placeGapConsistently " to Txt Box -> Click