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  • @SkyWarrior - amazing, thank you so much for your help. I am currently running your Perl script and will see what happens and how long it takes - fingers crossed!
  • as a follow-up I have tried running your GneomicsBDImport script and recieve this error: A USER ERROR has occurred: Failure working with the tmp directory /pub37/eve/Pararge_aegeria/1.trimmed/Index_1-501_701/practice/perl/./tmp. Try changing the tmp…
  • Ok thank you @SkyWarrior I will do. Also thank you for your perl scripts. I have never used perl before. Can I confirm that I am understanding it correctly? Your GenomicsBDImport script creates seperate databases per contig listed in your 'contigs…
  • At what sample size is it best to run GenomicsBDImport over CombineGCVFS? I will have a sample size of ~525 samples.
  • Ok thank you @bhanuGandham. Do you know why they might not be able to be calculated? Is it due to the low number of individuals (currently 3) I am testing it on?
  • Appologies for my delay in response. I have been doing fieldwork with limited internet. I have run: ``` for f in *.bam; do samtools index $f name=$(echo "$f" | cut -f 1 -d '.'); …
  • Hi @bhanuGandham Ok will give that a go no and let you know. Thank you Eve
  • Hello @Geraldine_VdAuwera , I am very new to GATK and I seem to be recieving this same error.. although I have specified "-ERC GVCF" in my HaplotypeCaller as below (the --annotation part is commented out as this causes another error...)…
  • Hi @bhanuGandham Thank you for your response. Does this mean I should change it to -DF DuplicateRead? What would happen if I simply run it without this? Thank you, Eve
  • > @Geraldine_VdAuwera said: > The -drf DuplicareRead command will tell tools to ignore the Sam flags that identify reads as duplicates, so you don't need to do any reprocessing. > > You only need to include it in tools that read…
  • @olavur - I have just re-run my haplotype caller without compressing it and its worked and has an index! :D will now work on using the whole genome. Thank you so much!
  • Hello @olavur - thank you so much for your speedy response! I am very new to GATK so thank you for your help. Ok, perhaps working on a compressed file is confusing matters. I will have a run through my test samples and make sure I am not creatin…
  • Hello Olavur, Thank you for your question and subsequent answer. I have recieved this same error but I was wondering how do I make an index for my gvcfs? Are the index files ".g.cf.gz.tai"? If so, then I have these and it must be anoth…