Retrieving ReMM scores via tabix

Pre-scored ReMM scores can be obtained without downloading the whole genome data set via Tabix:

#Specify score file link
SCORE_FILE=https://kircherlab.bihealth.org/download/ReMM/ReMM.v0.4.hg38.tsv.gz
#Download Tabix Index
INDEX=IndexFile
wget -c $SCORE_FILE.tbi -O $INDEX
#Retrieve variant scores
tabix $SCORE_FILE $INDEX chr22:1294989-1295247

The ReMM API for retrieving ReMM scores

Please note that this API is still experimental and not thought to be used for retrieving thousands of positions. For extensive use, please use our online or offline scoring or contact us. Thank you!

In addition to retrieving ReMM scores via tabix (see above), we also provide a webAPI. It is currently possible to retrieve genome ranges, single positions or single variants (SNVs and short InDels).

All API requests consist of a genome build, a ReMM version and the genome coordinates. The available genome builds are hg19 and hg38. Two ReMM score versions are available (v0.3.1.post1 and v0.4). If this information is omitted, version v0.4 is used.

Output format

When requesting ReMM scores via API you will retrieve a JOSN file. It has the always three items: result,structure and warnings. If something whent wrong there will be an error item with an error message. warnings are a list of warning strings (e.g. if too many positions are requested). The structure shows the structure of the result item. It differs bettween range/position to variant lookup. Position and ranges have the following structure:

"CHR:POS": Score

For variants it is like this:

"CHR:POS-REF-ALT": Score

Range and position access

Range access is similar to our web range lookup. It can be accessed via https://remm.bihealth.org/api/v1.0/<build>/<version>/<chrom>:<start>-<end> (using <chrom>-<start>-<end> is also possible).

A single position access is the same as range but without the <end> parameter. It can be accessed via https://remm.bihealth.org/api/v1.0/<build>/<version>/<chrom>:<position> (using <chrom>-<position> is also possible).

Example range

Command:

curl https://remm.bihealth.org/api/v1.0/hg38/v0.3.1.post1/chr5:1294989-1294999

Result:

{
  "result": {
    "chr5:1294989": 0.9796,
    "chr5:1294990": 0.878495,
    "chr5:1294991": 0.963492,
    "chr5:1294992": 0.94301,
    "chr5:1294993": 0.704851,
    "chr5:1294994": 0.923977,
    "chr5:1294995": 0.914086,
    "chr5:1294996": 0.889729,
    "chr5:1294997": 0.714331,
    "chr5:1294998": 0.545874,
    "chr5:1294999": 0.887858
  },
  "structure": {
    "CHR:POS": "SCORE"
  },
  "warnings": []
}

Example position

Command:

curl https://remm.bihealth.org/api/v1.0/hg38/v0.3.1.post1/chr5:1294989

Result:

{
  "result": {
    "chr5:1294989": 0.9796
  },
  "structure": {
    "CHR:POS": "SCORE"
  },
  "warnings": []
}

Variant access

Variant access is similar to our web variant lookup. It can be accessed via https://remm.bihealth.org/api/v1.0/<build>/<version>/<chrom>:<position>-<reference>-<alterantive> (using <chrom>-<position>-<reference>-<alterantive> is also possible).

For an SNV the ReMM score of its position is retrieved. For a multi nucleotide variant (MNV) the maximum over all positions is used. For InDels please use the previous nucleotide similar specified in the VCF file. For insertions the maximum of the preceding and subsequent nucleotide is retrieved. For deletions the maximum of the deleted nucleotied positions is retrieved. Please note that we do not check for correct of the alleles at the positions.

Example SNV

Command:

curl https://remm.bihealth.org/api/v1.0/hg38/v0.3.1.post1/chr5:1294989-T-C

Result:

{
  "result": {
    "chr5:1294989-T-C": 0.9796
  },
  "structure": {
    "CHR:POS-REF-ALT": "SCORE"
  },
  "warnings": []
}

Example Deletion

Command:

curl https://remm.bihealth.org/api/v1.0/hg38/v0.3.1.post1/chr5:1294989-TCGC-T

Result:

{
  "result": {
    "chr5:1294989-TCGC-T": 0.963492
  },
  "structure": {
    "CHR:POS-REF-ALT": "SCORE"
  },
  "warnings": []
}

Example Insertion

Command:

curl https://remm.bihealth.org/api/v1.0/hg38/v0.3.1.post1/chr5:1294989-T-TGGGGGCC

Result:

{
  "result": {
    "chr5:1294989-T-TGGGGGCC": 0.9796
  },
  "structure": {
    "CHR:POS-REF-ALT": "SCORE"
  },
  "warnings": []
}