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Helpful article. Thanks @Sheila !
Hi Sheila, That works! Thanks!
Hi team - Do you have any suggestions for the variant calling step (#6) and the hard filtering step (#7) for multisample RNAseq experiment aligned to a de novo transcriptome? Also, is there a still a benefit to using HaplotypeCaller over UnifiedGen…
In terms of best practices, do you have any suggestions? Currently, I plan to proceed with variant calling without performing the deduplication step, but I'm concerned with the bias that may create. Thanks for any input you can provide.
Hi everyone - I resolved this problem - the missing mate issue was generated when I used MarkDuplicates with option "REMOVE_DUPLICATES=TRUE", which appears to have created orphan reads in my outputted bam file. A Biostars discussion hypoth…
Hi @Geraldine_VDAuwera, To correct a missing mate problem, I ran the picard tool FixMateInformation as recommended above. However, running SamFileValidation shows that over 1M reads are still missing mate information. ERROR:MATE_NOT_FOUND 14570…
The last question I could find posted about this was here: https://gatkforums.broadinstitute.org/gatk/discussion/1692/calling-transcriptome-snp-with-gatk Has this special interest group been set up?
Can you provide specific reasons why GATK couldn't be used with a reference transcriptome instead of a genome?