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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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realignment command for alt contigs #397

Closed rod1Gene closed 1 year ago

rod1Gene commented 1 year ago

Do you have suggestions about the alignment program and arguments to use when realigning reads from alt contigs to chr6?

rod1Gene commented 1 year ago

For LILAC and its dependents.

charlesshale commented 1 year ago

The v38 alt-config ref genome is not currently supported. We recommend using the no-alt ref genome, especially for running Lilac. Lilac loads all known HLA alleles and internally considers all reads mapped to the HLA regions to these alleles.

rod1Gene commented 1 year ago

Thanks. Do you have an opinion about which aligner and arguments to use?

charlesshale commented 1 year ago

We use BWA version 0.7.17. The arguments are: mem -R SAMPLE_FLOWCELL_IDS -Y -t THREAD_COUNT REF_GENOME_FILE FASTQS

Our v38 ref genome is here: https://console.cloud.google.com/storage/browser/hmf-public/HMFtools-Resources/ref_genome/38/