Extracting Subsets Of Reads From A Bam File
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9.0 years ago
ijon.tichy ▴ 80

Hi, I have a large paired-end dataset in the BAM format and a list of read IDs which belong to a single mate of a pair. What I want to do is to extract their second mates from the whole dataset. Could you please advise me some efficient ways to do this like using, let's say, Bio-SamTools or something like that? Something memory- and time-efficient. Thanks!

bam samtools sequencing • 16k views
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how many reads-IDs do you have, does it fit in memory ?

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Just now it's only about 200. But for other datasets it could be much more, 10^3-10^5.

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9.0 years ago

2018: use picard https://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads


The following C++ code should filters only print the reads contained in your file (I've added to my variation toolkit http://code.google.com/p/variationtoolkit )

http://code.google.com/p/variationtoolkit/source/browse/trunk/src/bamgrepreads.cpp

Compilation:

g++ -O3 -Wall -I  path/to/samtool -L path/to/samtool bamgrepreads.cpp -lbam -lz

Usage:

./a.out -R file_containing_the_reads_name.txt (stdin|bam1 bam2...)

Options:

 -f INT   required flag
 -F INT   filtering flag
 -R FILE reads file
 -e  only one match per name (goes faster)
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Thank you! It works great!

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Does this take advantage of the queryname sorting order of a .bam file, or does it simply search through all the reads? Thanks!

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no, it searches 'all' the reads in the bam.

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Hi, I am trying to use this script, but somehow I can not compile it. seems the samtools I tried is not suitable for this script. Any suggestion that may be helpful?

Here are two error messages of my efforts.


shaoy@Darwin ~/rd/script $ g++ -O3 -Wall -I ~/rd/software/samtools-0.1.19 -L ~/rd/software/samtools-0.1.19 bamgrepreads.cpp -lbam -lz In file included from /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/ext/hash_set:61:0, from bamgrepreads.cpp:15: /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] /home/shaoy/rd/software/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt': /home/shaoy/rd/software/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create' /home/shaoy/rd/software/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy': /home/shaoy/rd/software/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join' collect2: error: ld returned 1 exit status

shaoy@Darwin ~/rd/script $ g++ -O3 -Wall -I ~/rd/software/samtools-1.0 -L ~/rd/software/samtools-1.0 bamgrepreads.cpp -lbam -lz In file included from /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/ext/hash_set:61:0, from bamgrepreads.cpp:15: /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] In file included from bamgrepreads.cpp:41:0: /home/shaoy/rd/software/samtools-1.0/bam.h:48:25: fatal error: htslib/bgzf.h: No such file or directory compilation terminated.
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whoa that's an old post. ThisĀ  C++ package is now obsolete, you'd better have a look at : https://github.com/lindenb/jvarkit/wiki/SamGrep

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and later: picard contains a tool to filter the reads using a list of read names.

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6.6 years ago
Fabio Marroni ★ 2.7k

I just ran in the same need, and I solved it using picard-tools:

java -jar FilterSamReads.jar INPUT=input.sam FILTER=includeReadList READ_LIST_FILE=reads_list.txt OUTPUT=selected_polym.sam

You can also give a look to this post.

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9.0 years ago
Geparada ★ 1.4k

If you're a python programmer, take a look to Pysam. There is a function called "mate" that can do what you're looking for.

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9.0 years ago
samtools view | grep -f

would work, though I can't vouch for how fast it will be.

It might be faster to grep out those reads from the fastq, and just realign them.

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That's exactly what I want to avoid. My datasets are very large and 'grep' takes a lot of time.

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7 weeks ago

Same as previous answers but another option to run Picard script with GATK. It works for me.

gatk FilterSamReads \
-I input.bam\
-O output.bam \
--READ_LIST_FILE read_names.txt \
--FILTER includeReadList
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