Error: invalid FORMAT field, "+"

[edgarsierraorozco]

Hello,

I ran Lumpy to find SVs in a tomato sample. As the Github page recommends, I tried using SVtyper to call the variants. However, I receive this issue: Error: invalid FORMAT field, "+" in SVtyper. Did I do something wrong in Lumpy?

Here is the code I used for lumpy:

Extract the discordant paired-end alignments.

samtools view -b -F 1294 LA1303_int2.bam > LA1303.discordants.unsorted.bam

Extract the split-read alignments

samtools view -h LA1303_int2.bam \ | /apps/lumpy/0.2.1/scripts/extractSplitReads_BwaMem -i stdin \ | samtools view -Sb - \

LA1303_int2.splitters.unsorted.bam

Sort both alignments

samtools sort LA1303.discordants.unsorted.bam LA1303_int2.discordants samtools sort LA1303_int2.splitters.unsorted.bam LA1303_int2.splitters

samtools view LA1303_int2.bam \ | tail -n+100000 \ | /apps/lumpy/0.2.1/scripts/pairend_distro.pl \ -r 101 \ -X 4 \ -N 10000 \ -o sample.lib1.histo

mean:248.459254074593 stdev:300.542984886694

lumpy \ -mw 4 \ -tt 0 \ -pe id:LA1303,bam_file:LA1303_int2.discordants.bam,histo_file:sample.lib1.histo,mean:248.459254074593,stdev:300.542984886694,read_length:151,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,min_mapping_threshold:20 \ -sr id:LA1303,bam_file:LA1303_int2.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20 \

LA1303_lumpy.vcf