terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr about freec HOT 8 OPEN

Hi dear, could you post the link of your hg19_snp142.SingleDiNucl.1based.txt file? I can't open the website now. Thanks a lot.

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https://mycore.core-cloud.net/index.php/s/fb8fb1ae01e5ffa2de210266a35374e9 - for the .vcf file that you can used instead of .txt and/or .bed

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@valeu thanks a lot

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Was this ever resolved? I'm getting the same error after the .cpn files are made and FREEC starts making the profiles.
EDIT: it might be my .bed file, making some changes and testing now

..FREEC will take into account only regions from /DATA/a.vliet/BMS/Melanoma_patients/FREEC_out/capture_region_illumina/TruSeq_Exome_TargetedRegions_v1.2.bed
..using GC-content to normalize copy number profiles
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr: __pos (which is 167) > this->size() (which is 0)```

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Please make sure that all coordinates come from the same genome build.

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Hi Valentina, my bams are aligned to hg38 and my .bed should also be... I just downloaded it from the Illumina website.
EDIT: trying another one just to be sure, since I do keep getting the error.

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To be sure that the capture file fits the data, you can visualize the .bam and the capture .bed in IGV.

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It worked with this other .bed! But the IGV visualization is definitely a good suggestion.

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