Hello everyone,
I am new in 1000 genomes project data. I want to download all bam files belonging to phase3, can anyone guide me how can I download all of them (from the command line?). Do you have any estimation how long it is going to take?
I want to compute the depth of coverage only for some specific intervals, not the entire genome. Is there any way that I could do it without downloading the data? I could find this, but not sure if it is relevant to what I want to do?
samtools view -b ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG01375/alignment/HG01375.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam 2:1,000,000-2,000,000 | genomeCoverageBed -ibam stdin -bg > coverage.bg
I would appreciate if anyone could guide me.
•
written
by
Pierre Lindenbaum
you wrote:
samtools view -b ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG01375/alignment/HG01375.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam 2:1,000,000-2,000,000 | (...)
you want:
samtools -bu view 'http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG01375/alignment/HG01375.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam' "2:1000000-2000000" | (...)
Thanks, so you mean I can use you command above without downloading the bam files?*
yes, nevertheless the index is downloaded (*.bai)
Can I also run it through loops for all of the bam files? there are 2504 individuals
to download the data, I just directly typed in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/ but could not download it!
get the paths from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree
For the loop I am trying this, but still I get warning message "no such file or directory"
for file in http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG*/alignment/*.bam;
do /data/programs/samtools-1.3.1/samtools view -c "${file}" 2:1000000-2000000
done
Am I doing something wrong here?
try:
wget -q -O - "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree" | cut -f 1 | grep '.bam$' | while read B; do echo -n "$B " && ~/packages/samtools/samtools view -c "http://ftp.1000genomes.ebi.ac.uk/vol1/$B" "2:1000000-2000000" && rm *.bam.bai ; done
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