Index 1 out of bounds for length 1

[mjko1210]

Thanks for this tool!

I was trying to merge two different SV calls and I got following errors:

So both vcf don't have records for chromosome2 (and many others as well) and I think that's why I see this error message. Is there any way to get around?

Thanks!

[mjko1210]

Hmm I'm actually getting this for many other samples. Although all chromosomes are present.

[mkirsche]

Hi,

Usually this is because of translocation or BND variants which do not indicate the chromosome of the second breakend involved in the variant (often denoted by the CHR2 INFO field). Would it be possible to post or send me one of the files which is causing the error so I can see more details about the format your VCF entries are in and see why it doesn't match the format Jasmine expects?

Thanks! Melanie

[mjko1210]

Thanks for your suggestions! I copied two vcf files that I was trying to merge here.

files_to_copy.zip

Thanks!

[mkirsche]

Hi,

Thanks for sending these files! It looks like the error is due to Jasmine not handling single breakends correctly (breakends which don't specify the other genomic position that the breakend is adjacent to). It looks like this is just a single variant in 01JHU528_2.gripss.filtered.vcf:

chr1 49530260 gridss4b_74384b A .TAAAAAAAAAAAAAAAAAAAA

I will work on adding support for this in the next day or two, and will post here once it is added!

Best, Melanie

[mjko1210]

Thank you so much!

[mkirsche]

Hi,

I have made a new release of version 1.1.5 which includes a fix for this. It will likely take up to a day before it gets through the bioconda review process and updates the version on there, but if you need to run Jasmine in the meantime the version on the Github repo should work. Please let me know if you continue to encounter issues with the new version!

Best, Melanie

[mjko1210]

Hi,

I just tested this with new git hub repo (with git pull).

However, this time, nothing was written from final vcf file.

Number of threads: 1 Merging complete - outputting results Number of sets with multiple variants: 0

My inputs are the same as before. However, this occurs even with the samples previously merged fine.

Do you have any idea?

Thanks, MJ

[mkirsche]

Hi MJ,

To clarify, are you getting an empty VCF output when you run the latest version of Jasmine? When I run Jasmine on the two files you provided, I get a VCF which contains all of the variants from both of the input files, but with none of them merged together because there are no pairs of SVs which are close together across the two files. If you are getting an empty VCF instead though, could you please let me know the exact command you are running, as well as which version number is output when you run Jasmine with no input parameters?

Thanks! Melanie

[mjko1210]

Thanks for your reply! yes, I'm getting exactly 0 byte size of file. Yeap, there is no overlap, so I just expect them to be simply merged. (union)

This was my command :

/fh/fast/ha_g/user/mko/tools/Jasmine/jasmine file_list=filelist_2.txt out_file=VY01JHU528_004_2T_merged.vcf

I also used sh build_no_iris.sh to install this.

Thanks again!

[mjko1210]

Jasmine version 1.1.5

[mkirsche]

Hi,

I am trying to replicate this by following the same commands, but I am not getting an empty file.

Number of threads: 1 Merging complete - outputting results Number of sets with multiple variants: 0

This output from your earlier message makes me think that your filelist_2.txt may be empty, as I get the same output when I run Jasmine on an empty filelist, and typically Jasmine lists the count of variants in each VCF file it is given. Could you please check that filelist_2.txt is a non-empty list of VCFs? When I run Jasmine on a list containing the two files you sent me I get the following output:

/home/mkirsche/Downloads/01JHU528_2.gripss.filtered.vcf has 9 variants /home/mkirsche/Downloads/VY01JHU528_004_2T.svaba.somatic.sv.vcf has 12 variants Number of threads: 1 Merging graph ID: chr10_chr10_TRA_++ Merging graph ID: chr10_chr10_TRA_-- Merging graph ID: chr12_chr12_TRA_++ Merging graph ID: chr12_chr12_TRA_-- Merging graph ID: chr14_chr14_TRA_++ Merging graph ID: chr14_chr14_TRA_-- Merging graph ID: chr17_chr17_TRA_++ Merging graph ID: chr17_chr17_TRA_-- Merging graph ID: chr17_chr8_TRA_++ Merging graph ID: chr17_chr8_TRA_-- Merging graph ID: chr18_chr18_TRA_++ Merging graph ID: chr18_chr18_TRA_-- Merging graph ID: chr18_chr8_TRA_-+ Merging graph ID: chr1_chr1_TRA_ Merging graph ID: chr1_chr1_TRA_-+ Merging graph ID: chr1_chr3_TRA_++ Merging graph ID: chr1_chr3_TRA_-- Merging graph ID: chr4_chr4_TRA_++ Merging graph ID: chr4_chr4_TRA_-- Merging complete - outputting results Number of sets with multiple variants: 0

Thanks, Melanie

[mjko1210]

Hi Melanie,

I just realized that I changed a path to file list when I ran this. Thanks for caught this! It would be nicer if the program throws some error message that it cannot locate a file. It works perfectly now!

Many thanks, MJ

[mkirsche]

Hi MJ,

I'm happy to hear that fixed your issue! I have updated the Github build of Jasmine to output a warning when passed a non-existent file list, and it will be integrated in the next version release as well.

Best, Melanie

[Qijie0615]

Thanks for this tool! I had the same problem. i try to merge deletion from different tools. i use a new release of version 1.1.5.