Place gap consistently

Yuan Li edited this page Jul 31, 2018 · 6 revisions

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 option.

  --placeGapConsistently (false)
               Place gaps consistently in alignments of a read as alignments
               of its reverse complementary sequence.

Toy example

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

From Data Management Page -> Click Analyze -> Select Resequencing from Analysis Application -> Click Advanced Analysis Parameters -> Identify Algorithm options Txt Box -> Add " --placeGapConsistently " to Txt Box -> Click OK

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