Running svtyper on Lumpyexpress vcf file

[btoe]

Hi I'm trying to run SVTyper on the vcf file I got after running Lumpyexpress. Here is the code that I am using:

svtyper \ -i sv.vcf \ -B sample.bam \ -l sample.bam.json \

sv.gt.vcf

I keep getting this error code: ValueError: fetch called on bamfile without index.

Am I suppose to index the bam file that came out of BWA-MEM? I am using svtyper 0.6.0. I was also wondering if its required to run svtyper on the Lumpyexpress vcf file or if its an optional step.

Thank you for your help!

[ryanlayer]

On Aug 9, 2018, at 8:55 PM, btoe notifications@github.com wrote:

Hi I'm trying to run SVTyper on the vcf file I got after running Lumpyexpress. Here is the code that I am using:

svtyper -i sv.vcf -B sample.bam -l sample.bam.json

sv.gt.vcf

I keep getting this error code: ValueError: fetch called on bamfile without index.

Am I suppose to index the bam file that came out of BWA-MEM?

Yes. SVTYPER needs the index. I am using svtyper 0.6.0. I was also wondering if its required to run svtyper on the Lumpyexpress vcf file or if its an optional step.

It is required there too.

Thank you for your help!

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[btoe]

Thank you so much for the response! So I ran svtyper using the indexed bam file and now I get a new error code:

Error: failed to build insert size histogram for paired-end reads. Please ensure BAM file (sample.bam) has inward facing, paired-end reads

I used this code from Lumpy github to align my data:

bwa mem -t 20 -R "@RG\tID:id\tSM:3790\tLB:lib" Mus_musculus.GRCm38.dna.primary_assembly.fa output_forward_paired.fq output_reverse_paired.fq \ | samblaster --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 | samtools view -Sb - > sample.bam

Thank you!!!!