specifing new target bed

[nitzankol]

I put a bed file called grch38_kit_name.bed in the reference_dir but I still get "ERROR Could not find intendended '.bed file ending' for target file '' . Is there a specific naming convention I need to follow? I have also tried to provide the file using the --exome_target_bed parameter but the program complains that it provided only for the first sample. I tried target.bed=ID1; target.bed=ID2;target.bed=ID3 . How should I use it to provide the target for all samples?

[jemten]

Hello @nitzankol 👋 It's a little cryptic but you can supply your own bed file using this command. Here sample 1 and 2 have one bed file and sample 3 another.

--exome_target_bed Agilent_SureSelect.V5.GRCh37.70_targets.bed=Sample1,Sample2 \
--exome_target_bed Agilent_SureSelectFocusedExome.V1.GRCh37_targets.bed=Sample3 \

[nitzankol]

Hi Andres, Thank you for your help. I hope you can help with my next problem - I get an error [FATAL] 2022/07/07 06:04:07 MIP_ANALYSE - Could not find intended vcfanno_config file: TEST_REFERENCES!/grch38_loqusdb_snvindel-2020-03-24-.vcf.gz I can't find where I need to define TEST_REFERENCES - I don't have it on my config.yaml

thank you very much Nitzan

‫בתאריך יום ב׳, 20 ביוני 2022 ב-12:57 מאת ‪Anders Jemt‬‏ <‪ @.***‬‏>:‬

Hello @nitzankol https://github.com/nitzankol 👋 It's a little cryptic but you can supply your own bed file using this command. Here sample 1 and 2 have one bed file and sample 3 another.

--exome_target_bed Agilent_SureSelect.V5.GRCh37.70_targets.bed=Sample1,Sample2 \

--exome_target_bed Agilent_SureSelectFocusedExome.V1.GRCh37_targets.bed=Sample3 \

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[jemten]

answered/closed in #1997