Pf3k pilot release 5
--------------------
Original date 2016-02-08
Last updated 2017-09-13

This directory contains data files comprising the Pf3k data release 5.  This
constitutes the final sample set for the pilot stage of the Pf3k project.

For more information about this data release, including terms of use and
guidance on how to cite the data, please see:

  http://www.malariagen.net/data/pf3k-5

This release contains an updated sample set (5.0) comprising 2640 Plasmodium
falciparum samples.  In addition to the release 4.0 set of:
    - 2375 samples from multiple sampling sites in Africa and
      Asia, contributed by a number of MalariaGen Pf Community Project studies.
    - 137 Senegal samples contributed by the Broad Institute.
    - 5 lab clonal samples (7G8, GB4, KH02, KE01, GN01) used for validation.

this release contains new samples contributed by MalariaGen Pf Community:
    - 96 lab clonal samples comprising parents and progeny from the Plasmodium
      falciparum genetic crosses project
    - 27 mixed lab strains in varying proportions created by Jason Wendler

It also contains a set of genotype calls for the 5.0 sample set.  These
genotypes are based on a de-novo variant discovery.  These genotypes should not
be taken as a quality-controlled output of the Pf3K project and are provided for
public interest and as a basis for future methods development. 


Files in the release include:

    - pf3k_release_5_metadata_20170804.txt.gz|xlsx : sample metadata file in
      gzipped tab-delimited and excel formats
    - pf3k_release_5_crosses_metadata.txt|xls : sample metadata file specific to
      98 crosses samples in tab-delimited and excel formats
    - pf3k_release_5_mixtures_metadata.txt|xls : sample metadata file specific to
      27 mixture samples in tab-delimited and excel formats
    - Pfalciparum.genome.fasta.gz : 3D7 v3.1 reference genome sequences (downloaded from
      ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/2015-08/Pfalciparum.genome.fasta.gz)
    - Pfalciparum.genome.fasta.gz.md5 : checksum for reference genome
    - BAM/[samplename].bam - analysis BAM files, one-per-sample, aligned to the
      3D7_v3 reference
    - BAM/md5.txt - checksums for BAM files
    - 5.1/SNP_INDEL_[chromosome].combined.filtered.vcf.gz : vcf files,
      one-per-chromosome, for release 5.0 genotypes
    - 5.1/md5.txt : checksums for vcfs
    - deprecated_metadata/pf3k_release_5_metadata.txt|xls : older sample
      metadata file in tab-delimited and excel formats

Note on sample metadata - this release was originally accompanied by the sample
metadata found in deprecated_metadata/pf3k_release_5_metadata.txt|xls. We
subsequently received updates on metadata of collection sites and dates from
some partners. To guarantee consistency across samples, we have replaced
collection date with collection year, which is now populated for all samples,
and which is a proxy for season. The correct sample metadata to use with this
release is pf3k_release_5_metadata_20170804.txt.gz|xlsx. In addition to the
changes to site and collection year, this file includes three additional
columns. IsFieldSample is set to True for field samples and False for lab
samples. The data set includes some replicate samples (multiple sequencing of
samples from the same individual). The PreferredSample column is set to True
for the sample from each individual which has the greatest coverage. For most
population analysis, the sample set should be restricted to samples where this
is True. The AllSamplesThisIndividual column can be used to identify which
samples come from the same individual. As an example, samples PF0550-C and
PF0550-Cx both come from the same individual. PF0550-C is the preferred sample
for analysis in this case.

See additional README files for further details.