smoove
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Required tag PRPOS not found
Dear @brentp I used the following command to run Smoove on my several thousands of samples: $SMOOVE call --outdir $OUTDIR --exclude $BED --name $ID -f $REF -p 1 --genotype $BAM
but when merging Smoove SV calls of all samples, the program exited with exit status 1 and this error message: Required tag PRPOS not found. Please ensure you've run lumpy withthe -P option to emit breakpoint probabilities.
Is there anything I forgot to do in SV calling step? I hope I won't have to do calling SVs again as the number of samples is quite high. Any help would be highly appreciated.
Best, Saeideh
Hi, can you show the commands you run (just for one sample is fine) and the output you got? This can mean that one or a few samples have truncated files. As a start you could try:
zgrep -cv ^# /path/to/*.persample.vcf.gz
and see if any samples have fewer than expected rows.
Dear @brentp
Thank you so much for your prompt reply. The result of zgrep command for most of samples was between 3700-7000 but for 100 samples it was exactly 29,016! So, I repeated the SV calling for those 100 samples again and now the range is 3700-7000 for all of them and merging step is being run. Thank you for your kind help.
Just another question: the merging command is taking a long time (which I expected as the number of samples is quite high [11,000 samples]), it's 25 hours now. I just wanted to know if there is any other way for doing this step so that it takes a shorter time (something like dividing samples into batches etc.).
Best, Saeideh
Hi Saeideh, yes, you can divide into batches to improve the merging time. I would like to improve this at some point, but for now, you'll have to write your own code to do the merging in smaller batches.
I am glad to hear that you got the previous problem sorted.