Error: Segmentation fault (core dumped) (sorting with picardtools)

Hi Fritz,

I am working a bacterial genome, which is a circular genome. I would like to call SV using Sniffle.

I have mapped my PacBio read to ref genome using NG-MLR. ngmlr -r $REF -q $FILE -o $OUTPATH/$SAMNAME -t 30

Then I sort the sam file and convert it to sorted bam format using picard tool. java -Djava.io.tmpdir=pwd/tmp -jar $PICARD/picard.jar SortSam \ I=$OUTPATH/$SAMNAME O=$OUTPATH/${SAMNAME%%.sam}_sorted.bam \ SO=coordinate TMP_DIR=pwd/tmp

The sorted bam file was fed to Sniffles:

sniffles -m file_sorted.bam -v file.vcf

After running this command, I got an error message: Segmentation fault (core dumped)

Could you help me with this problem?

Jie

[fritzsedlazeck]

50x is more than enough.

There are no dumb questions. Yes gt is gebotype estimation. You can maybe use it and filter out het SVs. 0/1 Cheers Fritz

[colinbrislawn]

Thank you for your fast feedback!

I have about 50x coverage, all from nanopore (noisy but long).

assumes a diploid organism for predicting GT.

At the risk of asking a dumb question… What is GT in this context? Genotype? How would this assumption conflict with a haploid organism like E. coli?

Thanks!