This page contains links to bam and gvcf files, as well as relevant index files, for all 20,864 samples from Pf7. Files can be downloaded direct from the links, or can also be downloaded as part of a script, e.g. by using a command such as wget https://pf7_release.cog.sanger.ac.uk/gvcf/FP0008-C.g.vcf.gz . If using this data, please cite the Pf7 manuscript. More details on the Pf7 data resource, including sample metadata and genotype calls, can be found at https://www.malariagen.net/resource/34.
Bam files are the final sample-level bams created as part of the pipeline. These differ in a number of ways from the raw bam/cram files available at the ENA. For example we have remapped all reads to the latest reference genome, fixed mates and marked duplicates, run GATK’s BQSR and merged lanes where a sample had more than one lane of sequencing data. Gvcf files are the output of running GATK’s HaplotypeCaller. This could be useful if you would like to create a joint call set of Pf7 and your own sequencing data.
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