List Of Ftp Urls For Bam Files From 1000G Project With Read Length Above 70 And Coverage Above 20X

Question

[Ahdf-Lell-Kocks]

How can I get a list of ftp URLs for bam files from the 1000g project where the individual was resequenced with read length above 70 and coverage above 20x?

I would like to then use the ftp URL in samtools like: samtools view ftp://something.something/blah/blah/file.bam

Any ideas?

Answer 1

[lh3]

You should have a look at:

ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase1/phase1.alignment.index

ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase1/phase1.alignment.index.bas.gz

However, only a couple samples meet your requirement. 1000g does low-coverage sequencing. The fundamental philosophy is not to waste money on high coverage. You should go to SRA. There are more decent samples.