Call specific mutations in reads:

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1

Hello,

I am trying to use the tool “Call specific mutations in reads” to calculate frequencies and stats of mutations in my dataset. However, when I run this tool it aborts due to the error:

[W::hts_idx_load2] The index file is older than the data file: bam_input.bam.bai
[W::vcf_parse] Contig 'Amplified' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::hts_idx_load2] The index file is older than the data file: bam_input.bam.bai
[W::hts_idx_load2] The index file is older than the data file: bam_input.bam.bai
/data/jwd02f/main/072/274/72274460/tool_script.sh: line 77: 126887 Killed                  python '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/variant_analyzer/3f1dbd2c59bf/variant_analyzer/read2mut.py' --mutFile '/data/dnb10/galaxy_db/files/9/0/e/dataset_90e6ab01-620f-445f-8bb5-74e7d3ac0688.dat' --bamFile bam_input.bam --inputJson '/data/dnb10/galaxy_db/files/1/3/a/dataset_13a3ca74-504f-43e4-b71f-b8aedfcecffd.dat' --sscsJson '/data/dnb10/galaxy_db/files/0/3/b/dataset_03bbfecb-33c7-4129-b27d-978f5d00832b.dat' --thresh '0' --phred '20' --trim '10' --outputFile '/data/jwd02f/main/072/274/72274460/outputs/dataset_d25b0b01-9b6f-4373-8564-ec82ee41362b.dat'

Does anybody know what I can try to do to fix this?

Thank you in advance!

2

Welcome, @Kristel !

This is the part I would suggest paying attention to first:

Contig ‘Amplified’ is not defined in the header.

When working with VCF data, any of the reference sequences present in the first column of the data lines needs to also be defined at the top of the file, in the VCF header.

Check your file – my guess is that you lost the header, or maybe replaced the header, and there is some mismatch now?

You can share your work if you get stuck. A shared history link and maybe a tutorial link if you are following one. How to do that is in the banner at this forum, also here → How to get faster help with your question

Please let us know how this works out! :scientist: