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Submiters of samples in 1000 genomes project

Hello!

I am trying to discover which capture kit was used for some BAM files I obtain from the public 1000 genomes repositories (e.g. HG00096). Currently, I am going through their volume mounted on S3, so I cannot give an easy link, but I am going someone knows their way around this data.

I have found that there are several submitters, and each submitter has their own capture kit in the paper supplementary: https://media.nature.com/original/nature-assets/nature/journal/v526/n7571/extref/nature15393-s1.pdf

How would one discover which samples were submitted by which center/contributor? IS there an easier way to find out which capture kit was used?

Thanks in advance!

EDIT: The data is given at ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/.

1000 genomes metadata
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by ognjen011 ognjen011

1 answer

you can find the sequencing center in the read group of the bam files:

$ curl -s  "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree" |grep bam | cut -f 1 | grep 'bam$' | grep HG00096 | sed 's%^%ftp://ftp.1000genomes.ebi.ac.uk/vol1/%' | while read U; do echo ${U} && curl -s "${U}" | samtools view -H | grep '^@RG' | tr "\t" "\n" | grep '^CN' | cut -d ':' -f 2 | sort | uniq ; done

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/high_coverage_alignment/HG00096.wgs.ILLUMINA.bwa.GBR.high_cov_pcr_free.20140203.bam
BI
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/exome_alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.exome.20120522.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/exome_alignment/HG00096.unmapped.ILLUMINA.bwa.GBR.exome.20120522.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/exome_alignment/HG00096.chrom11.ILLUMINA.bwa.GBR.exome.20120522.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/alignment/HG00096.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/alignment/HG00096.unmapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/technical/ncbi_varpipe_data/alignment/HG00096/HG00096.ILLUMINA.mosaik.GBR.low_coverage.20101123.bam
wugsc
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/technical/ncbi_varpipe_data/alignment/HG00096/HG00096.chrom20.ILLUMINA.mosaik.GBR.low_coverage.20101123.bam
wugsc
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/technical/other_exome_alignments/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.BWA.GBR.exome.20110411.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/exome_alignment/HG00096.mapped.illumina.mosaik.GBR.exome.20110411.bam
wugsc
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.unmapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
WUGSC
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/ncbi_varpipe_data/alignment/HG00096/HG00096.mapped.illumina.mosaik.GBR.low_coverage.20111114.bam
wugsc
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/ncbi_varpipe_data/alignment/HG00096/HG00096.chrom11.illumina.mosaik.GBR.low_coverage.20111114.bam
wugsc
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/ncbi_varpipe_data/alignment/HG00096/HG00096.chrom20.illumina.mosaik.GBR.low_coverage.20111114.bam
wugsc
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/other_exome_alignments/HG00096/exome_alignment/HG00096.mapped.illumina.mosaik.GBR.exome.20111114.bam
wugsc
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140203_broad_high_cov_pcr_free_validation/matching_LC_samples_bwamem/HG00096.bwa_mem.20130502.low_coverage.20140501.bam
WUGSC
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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you very much!

• 0 views • link
written by ognjen011 ognjen011

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