STAR mapping + GATK

[Angelven]

Hi Qing,

As you said in Issues #21 , multi-mapping to a combined alignments and strict criterion were used to get the real SNVs and these can be replaced by other methods such as GATK. So should I run the STAR mapping + GATK pipeline instead of multi-mapping to combined alignment + Samtools 'pileup' program ? a best-practice for variant discovery in RNA-seq as descripted in GATK team.

Best, Li

[zhqingit]

Hi Li,

Yes, the alignment and snv calling steps are independent to GIREMI. So you can try STAR+GATK. Make sure the errors have been removes.

Best, Qing

2016-10-17 18:01 GMT-07:00 Angelven notifications@github.com:

Hi Qing,

As you said in Issues #21 https://github.com/zhqingit/giremi/issues/21 , multi-mapping to a combined alignments and strict criterion were used to get the real SNVs and these can be replaced by other methods such as GATK. So should I run the STAR mapping + GATK pipeline instead of multi-mapping to combined alignment + Samtools 'pileup' program ? a best-practice for variant discovery in RNA-seq as descripted in GATK team.

Best, Li

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[Angelven]

Hi Qing,

Thanks for your help.

Best wishes, Li

[Angelven]

Hi Qing,

Another question, to reduce the running time, shall I split the .bam file into 24 chromosome and then run GIREMI, separately ?

Best, Li

[zhqingit]

Hi Li,

Don't split the bam file. Better keep them together for the estimation of the MI distribution.

Best, Qing

2016-10-18 5:34 GMT-07:00 Angelven notifications@github.com:

Hi Qing,

Another question, to reduce the running time, shall I split the .bam file into 24 chromosome and then run GIREMI, separately ?

Best, Li

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[JohnMCMa]

There's a thing about GATK I'm like to mention. Since GATK performs indel realignment for HaplotypeCaller or MuTect2 functions, I have some doubt on whether the original input BAM would be an appropriate input. Please explore the option --bamout used in these functions and use an appropriately processed bamout for GIREMI purposes.

This does not apply if you use UnifiedGenotyper.