BAM FILE FORMAT DECOMPRESSION FULL SIZE
BAM FILE FORMAT DECOMPRESSION PLUS
BAM FILE FORMAT DECOMPRESSION DOWNLOAD

It should be interesting.Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and Bob Handsaker et al. But with two, you can compare their results to each other. With just one test, you canРІР‚в„ўt tell how good it is. Once I get the long read results, IРІР‚в„ўll look at the BAM and FASTQ files from both tests, compare them to each other, and see what I can learn from them. I think IРІР‚в„ўm going to wait until I get the results from my Long Read test. I purchased the Long Read WGS test from Dante a few days ago. These files are in a different format than the two VCF files I downloaded for SNPs and INDELs earlier. Basically, these are various files indicating all my gene, exome and genome differences from the human reference for both my SNPs and my INDELs (insertions/deletions).

They contain a number of files, some gzipped (which I decompressed in the above listing). There are four subdirectories named sv, snp, indel and cnv: IРІР‚в„ўll have to look that up again if I ever have to use them. I used to know what paired reads are, but I forgot.

Insert size has something to do with the analysis process. This directory also contains the same summary xls file that was with the FASTQ files (see above) and three png images:Р”Р„ that shows that I mostly achieved at least 30x coverageР”Р„ that shows the cumulative distribution of the depth The BAM index file allows the programs to go directly to the section of the genome that the analysis program needs. For most purposes, you donРІР‚в„ўt want to decompress this file since most genome analysis programs work with the BAM file itself and with a small bam.bai (BAM index) file of 8 MB that is also in the directory. Decompression time for this file on my computer is over 17 hours. It is 115 GB in size compressed at 27% which expands to 425 GB. The result_alignment directory contains the aaaaaaaaaaaaaa.bam file. Most of this is all new to me too, so I canРІР‚в„ўt explain what all this means yet. In order to get an average of 30x coverage on 3 billion base pairs, I figure the average read length would have to be 60 base pairs.Р”В®ach of the eight 5mm files have two pictures associated with them that show some results, e.g.Р”Р„nd aaaaaaaaaaa_L01_ contains:

BAM FILE FORMAT DECOMPRESSION PLUS

The first line of each group of 4 is an identifier, the 2nd are exactly 100 base pari values, the 3rd is just a plus (at least in the records I glanced at) and the 4th are codes that represent the quality of each of the 100 reads.Р”Р„lso in the directory is a small excel file that contains some summary statistics from my WGS test. Shown above are the first 4 groups of readings in one of the files, where 4 lines make up a reading. HereРІР‚в„ўs what the beginning of one of the unzipped FASTQ files looks like:

BAM FILE FORMAT DECOMPRESSION FULL SIZE

I have a fast Intel i7 computer and it takes 30 minutes to uncompress one of these files to its full size of about 22 GB. Where aaa is some identifier, and mm run from 78 to 85 and n is 1 or 2.Р”В®ach file is about 8 GB in size and is gzip compressed at about 34%. The clean_data directory contains 16 files named something like:

As a result they were sent to me on the large hard drive. The files supplied this time include all my data, not just the variants. the readings where I vary from the human genome reference. The VCF (Variant Call Format) files only contain the variants, i.e. Those files were compressed and totaled 224 MB and expanded to 869 MB. I reported on the files a couple of months ago in my post: My Whole Genome Sequencing.

BAM FILE FORMAT DECOMPRESSION DOWNLOAD

Previously I was able to download my VCF files from DanteРІР‚в„ўs site. It was shipped from their lab in Italy and came on a 1 TB hard drive.

I received the rest of my raw data files for my WGS (Whole Genome Sequencing) test today.

Bam file format decompression