Custom BED file causes an error

If you use import a custom BED file into Ion Reporter™ Software, the file is validated. The following errors indicate that there is a problem with the BED file. To resolve an error, review the BED file, and edit the BED file if necessary. Contact your Field Bioinformatics Specialist (FBS) for further assistance with troubleshooting BED files.

Observation

Possible cause

Recommended action

Error parsing track line key=value pairs

There is an error for in the key values that are used in the track line. Example key value pairs are: track name="HSMv12.1" description="AmpliSeq Pool HSMv12.1" version="Ampliseq.com1.0" type="bedDetail".

Review the BED file and ensure that the value pairs are correct.

Error parsing track line, no closing quotes

The closing quotes are missing from the key value pair in the first line (track line) of the BED file. For example: track name="HSMv12.1" description="AmpliSeq Pool HSMv12.1" version="Ampliseq.com1.0" type=bedDetail.

Review the track line and add closing quotes.

ionVersion track key is only valid with type=bedDetail

A BED file that includes an IonVersion field must also have a type=bedDetail field.

Review the first line (track line) of the BED file and ensure that the type=bedDetail and the ionVerison field are included.

Field OBS cannot be the same as REF

The strings used in the OBS and REF fields cannot be the same. Both fields cannot be ATC, for example.

Change OBS=string so that it is not the same as the REF=string.

Inconsistent number of columns

Every line in the BED file must include the same number of columns.

Review the BED file and ensure that every line in the file has the same number of columns.

BED track line only allowed in the first line: All lines ignored after this one

BED files allow only one track line in the first line of the header. An example track line is: track name="HSMv12.1" description="AmpliSeq Pool HSMv12.1" version="Ampliseq.com1.0" type=bedDetail".

Remove the redundant track line.

Line length exceeds 64K

A line in the BED file exceeds 64K characters.

Review the BED file and reduce the line length so that it is 64K or less.

Unknown chromosome name

A chromosome name in the BED file is not included in the FASTA file.

Review the BED file and provide the correct chromosome name.

Region start not in a valid range

For hotspot BED file, the region start value is not in a targeted BED region.

Remove this line.

Region end not in a valid range

For hotspots BED file, the region end value is not in a target bed region.

Remove this line.

Region start and end in reverse order

The region end has a smaller value than the value for the start region.

Ensure that the value for the region start has a smaller value than the value for the end region.

Detail BED file with type=bedDetail must have between 5 and 14 columns

The numbers of columns in a Detail BED file that includes type=bedDetail must have between 5 and 14 columns

Review the number of columns in the BED file and ensure that there are between 5 and 14 columns.

Hotspots BED file must have format type=bed

Information is missing from the header of the BED file.

Add format type=bedDetail to the file header of the hotspots BED file.

BED file without type=bedDetail must have between 3 and 12 columns

The number of columns for a BED file without type=bedDetail has the incorrect number of columns

Review the number of columns in the BED file and ensure that there are between 3 and 12 columns.

BED file contains no usable regions

The BED file might be empty, or every line has at least one error.

Ensure that you are using a BED file that is valid and correctly formatted.

REF field contains characters other than ATCGatcg

The alpha-numeric characters ATCG, or atcg, are not used in the REF field.

Find the REF field in the custom BAM file. Ensure that the field is populated with characters that use the format ATCG or atcg.

OBS field contains characters other than ATCGatcg

The alpha-numeric characters ATCG, or atcg, are not used in the OBS field.

Find the OBS field in the custom BAM file. Ensure that the field is populated with characters that use the format ATCG or atcg.

ANCHOR field contains characters other than ATCGatcg

The alpha-numeric characters ATCG, or atcg, are not used in the ANCHOR field.

Find the ANCHOR field in the custom BAM file. Ensure that the field is populated with characters that use the format ATCG or atcg.

REF field does not match content of reference fasta file

The string for the REF sequence does not match the reference file.

Look at the REF=string and ensure that string is the as the one at that position of the reference sequence from the FASTA file

Mandatory OBS field not found

A field is missing from the custom BED file.

Add an OBS field to the custom BAM file. Ensure that the field is populated with characters that use the format ATCG or atcg.