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Split A Bam File Into Smaller Files By Tile Number

Hi all,

I would like to split a very big BAM file into smaller files for the purpose of annotating it in parallell. Someone suggested splitting it by tile number, which is a good idea since that guarantees that all the alignments for a given read are contained within the same file.

However, I am stuck as to how to phrase the awk command for this purpose, since the tile number is contained within the READ ID string in the first filed of the alignment, separated from the other information in the string by ":" , while this field is separated from the other fields by "\t" .

HWI-ST975:104:C0W47ACXX:8:1101:8269:91631

Tile number (encrypted) = 1101 (5th field) How could I use awk to get each line put into its new corresponding file based on its tile number?

Thanks, Carmen

samtools tophat
• 4,198 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by gaelgarcia05 gaelgarcia05

I think i may have a perl solution to this, but I don't know the exact way to phrase the output. Can anybody help me out ? :)

I have made a hash of hashes, where all the lines of a file are sorted into a key of the "master" hash depending on the value of their 5th field.

%Tiles has n keys, where each key is a different $Tile_Number.

Each $Tile_Number opens a new hash that contains all lines whose $Tile_Number was the right number of the current key. The value of each of these new keys (lines) is just 1.

$Tiles{Tile_Number}($Line}=1 , where $Tiles{Tile_Number} has many $Line=1 entries.

I want to print each $Tiles{$Tile_Number} hash in a separate file, preferably, creating the file upon the creation of the $Tile_Number key, and printing as each new $Tiles{$Tile_Number}{$Line}=1 is added, to save memory. The best would be to not print the final value (1), but I can do away with this, I guess..

How can I tell perl to open a new file for each key in the "master" hash and print all of its keys?

Thank you, Carmen

• 0 views • link
written by gaelgarcia05 gaelgarcia05

2 answers

I just wrote a java program to split a BAM by tile:

https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/splitbytitle/SplitByTile.java

it uses the picard library to parse the BAM.

Compilation:

cd src/main/java
javac -cp path/to/picard.jar:path/to.sam.jar com/github/lindenb/jvarkit/tools/splitbytitle/SplitByTile.java

Execute

java  -cp path/to/picard.jar:path/to.sam.jar \
com.github.lindenb.jvarkit.tools.splitbytitle.SplitByTile \
I=my.bam O=tmp/TILE__TILE__/jeter.__TILE__.bam CREATE_INDEX=true
• 28 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

WOW, cool! Let me check it out, Pierre!

• 0 views • link
written by gaelgarcia05 gaelgarcia05

I think i may have a perl solution to this, but I don't know the exact way to phrase the output. Can anybody help me out ? :)

I have made a hash of hashes, where all the lines of a file are sorted into a key of the "master" hash depending on the value of their 5th field.

%Tiles has n keys, where each key is a different $Tile_Number.

Each $Tile_Number opens a new hash that contains all lines whose $Tile_Number was the right number of the current key. The value of each of these new keys (lines) is just 1.

$Tiles{Tile_Number}($Line}=1 , where $Tiles{Tile_Number} has many $Line=1 entries.

I want to print each $Tiles{$Tile_Number} hash in a separate file, preferably, creating the file upon the creation of the $Tile_Number key, and printing as each new $Tiles{$Tile_Number}{$Line}=1 is added, to save memory. The best would be to not print the final value (1), but I can do away with this, I guess..

How can I tell perl to open a new file for each key in the "master" hash and print all of its keys?

Thank you, Carmen

• 0 views • link
written by gaelgarcia05 gaelgarcia05

This is not an answer to the question. Please add this content to your original question and delete this answer.

When you add information as an answer like this, it flags the question as answered and people may not notice that your question has gone unanswered.

• 17 views • link
written by Josh Herr Josh Herr

Thanks for letting me know!

• 0 views • link
written by gaelgarcia05 gaelgarcia05

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