PacBio data

[Jana]

Hi,

just a general question about platypus. Is it possible to use it for PacBio data? I am especially interested in genotyping given SNPs but when I tried, it always returned an empty vcf file. This is the command I used:

python Platypus/bin/Platypus.py callVariants --bamFiles=pacbio_reads.bam --refFile=reference.fa --output=output.vcf --source=variants.vcf.gz --minPosterior=0 --getVariantsFromBAMs=0

Best,
Jana

[Andy Rimmer]

Hi Jana,

I haven't tried to use Platypus on PacBio data. It wasn't designed for that use case, but in principle it should work. There might be some default constraints on read length that need turning off. Can you post the log file? If there's nothing informative in the log file try running with --verbosity=3 (or higher).

Kind regards,

Andy

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Dr Andrew (Andy) Rimmer

[Jana]

Hi Andy,

this is the log-file I get:

2017-10-05 10:50:01,401 - INFO - Beginning variant calling
2017-10-05 10:50:01,401 - INFO - Output will go to results_platypus/output.vcf
2017-10-05 10:50:01,508 - DEBUG - Loaded regions from BAM header, SQ tags
2017-10-05 10:50:01,508 - DEBUG - 196 regions will be searched
2017-10-05 10:50:01,680 - DEBUG - Found multiple read group tags in file hg38.NA12878.bam
2017-10-05 10:50:01,680 - DEBUG - Adding sample name NA12878, using BAM RG:SM tag in file hg38.NA12878.bam
2017-10-05 10:50:01,681 - DEBUG - Max haplotypes used for initial haplotype filtering = 50
2017-10-05 10:50:01,681 - DEBUG - Max haplotypes used for genotype generation = 50
2017-10-05 10:50:01,681 - DEBUG - Max genotypes = 1275
2017-10-05 10:50:01,689 - INFO - Processing region NC_007605.1:0-100000. (Only printing this message every 10 regions of size 100000)
2017-10-05 10:50:01,690 - DEBUG - There is one sample in each BAM file. No merging is required
2017-10-05 10:50:02,688 - INFO - Merging output VCF file(s) into final file results_platypus/output.vcf
2017-10-05 10:50:02,689 - INFO - Finished merging VCF file(s)
2017-10-05 10:50:02,689 - INFO - Finished variant calling

If I use --verbosity=3, it additionally prints a large number of regions.

Best,
Jana

Am Donnerstag, 5. Oktober 2017 09:28:59 UTC+2 schrieb Andy Rimmer:

Hi Jana,

I haven't tried to use Platypus on PacBio data. It wasn't designed for that use case, but in principle it should work. There might be some default constraints on read length that need turning off. Can you post the log file? If there's nothing informative in the log file try running with --verbosity=3 (or higher).

Kind regards,

Andy

On Wed, Oct 4, 2017 at 4:19 PM, Jana <eble...@gmail.com> wrote:

Hi,

just a general question about platypus. Is it possible to use it for PacBio data? I am especially interested in genotyping given SNPs but when I tried, it always returned an empty vcf file. This is the command I used:

python Platypus/bin/Platypus.py callVariants --bamFiles=pacbio_reads.bam --refFile=reference.fa --output=output.vcf --source=variants.vcf.gz --minPosterior=0 --getVariantsFromBAMs=0

Best,
Jana

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