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Variant calling on 454 data

psb21psb21 BejaMember

Hello,

I read in the Realigner Target Creator page that this tool will not work on 454 reads due to the presence of false indels inherent to the technology, but i still tried it to check the quality of my mappings. Below is an example of one of the results in one sample:

INFO 21:13:47,410 MicroScheduler - 526217 reads were filtered out during the traversal out of approximately 526217 total reads (100.00%)
INFO 21:13:47,411 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 21:13:47,411 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter
INFO 21:13:47,412 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 21:13:47,412 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 21:13:47,413 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 21:13:47,414 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 21:13:47,414 MicroScheduler - -> 175060 reads (33.27% of total) failing MappingQualityZeroFilter
INFO 21:13:47,415 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 21:13:47,416 MicroScheduler - -> 351157 reads (66.73% of total) failing Platform454Filter
INFO 21:13:47,416 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
INFO 21:13:51,655 GATKRunReport - Uploaded run statistics report to AWS S3

The 33.27% might refer to the reads that mapped in more than one location, i will look at them later, but i would like to know what does the "Platform454Filter" really do, i couldn't find any description here.

Furthermore, do you recommend any best practices for calling vairants with this technology ? Particularly, in the removing duplicates step, does it make a big difference not removing duplicates with single end reads ?

I would appreciate any help on this.
Thanks in advance,
Pedro Barbosa

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