three alternate alleles for a diploid genotype?

[Katherine Wilkins]

Hello,

I have used platypus to call genotypes in Genome In a Bottle sample HG001/NA12878 and I get the following line in my output:

1	8446082	.	ATTTTTTTT	A,ATTTTTTTTTTT,TTTTTTTTT	985	SC;HapScore;badReads	BRF=0.0;FR=0.5000,0.4989,0.5000;HP=21;HapScore=12;MGOF=20;MMLQ=7;MQ=70.0;NF=4,4,1;NR=7,7,3;PP=363,23,985;QD=33.2727272727;SC=ATATATATATATTTTTTTTTT;SbPval=0.54;Source=Platypus;TC=12;TCF=4;TCR=8;TR=11,11,4;WE=8446102;WS=8446072	GT:GL:GOF:GQ:NR:NV	1/2:-1,-1,-1:20:4:12,12,15:11,11,4

Given that the genotype indicates that only alternate alleles 1 and 2 are present, I'm not sure why platypus returns a third alternate allele. Any help interpreting this output or identifying it as bug would be appreciated. Thanks!

Best,

Katie

[Andy Rimmer]

Hi Katherine,

Platypus will list all the alleles that have more than a certain amount of support in the data (default is minimum of 2 supporting reads and phred-scaled posterior > 5), which can lead to > 2 alternate alleles being listed. This is not a bug. It looks like this region contains a long T homopolymer, which will probably lead to a large number of sequencing indel errors, on top of whatever actual variation exists. Calling indels correctly in these regions is difficult and error-prone, but the best way to interpret this is to use the called genotype and ignore anything else. So in this case, Platypus has called the first 2 alternate alleles (the 1/2 genotype), and the 3rd should be ignored.

Kind regards,

Andy

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Dr Andrew (Andy) Rimmer

[Katherine Wilkins]

Thanks, Andy! That makes sense.

Best,

Katie

On Monday, April 3, 2017 at 5:25:11 AM UTC-7, Andy Rimmer wrote:

Hi Katherine,

Platypus will list all the alleles that have more than a certain amount of support in the data (default is minimum of 2 supporting reads and phred-scaled posterior > 5), which can lead to > 2 alternate alleles being listed. This is not a bug. It looks like this region contains a long T homopolymer, which will probably lead to a large number of sequencing indel errors, on top of whatever actual variation exists. Calling indels correctly in these regions is difficult and error-prone, but the best way to interpret this is to use the called genotype and ignore anything else. So in this case, Platypus has called the first 2 alternate alleles (the 1/2 genotype), and the 3rd should be ignored.

Kind regards,

Andy

On Fri, Mar 31, 2017 at 6:41 PM, Katherine Wilkins <kawilkin...@gmail.com> wrote:

Hello,

I have used platypus to call genotypes in Genome In a Bottle sample HG001/NA12878 and I get the following line in my output:

1	8446082	.	ATTTTTTTT	A,ATTTTTTTTTTT,TTTTTTTTT	985	SC;HapScore;badReads	BRF=0.0;FR=0.5000,0.4989,0.5000;HP=21;HapScore=12;MGOF=20;MMLQ=7;MQ=70.0;NF=4,4,1;NR=7,7,3;PP=363,23,985;QD=33.2727272727;SC=ATATATATATATTTTTTTTTT;SbPval=0.54;Source=Platypus;TC=12;TCF=4;TCR=8;TR=11,11,4;WE=8446102;WS=8446072	GT:GL:GOF:GQ:NR:NV	1/2:-1,-1,-1:20:4:12,12,15:11,11,4

Given that the genotype indicates that only alternate alleles 1 and 2 are present, I'm not sure why platypus returns a third alternate allele. Any help interpreting this output or identifying it as bug would be appreciated. Thanks!

Best,

Katie

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