Capturing clusters having T to C mutation

Question: Capturing clusters having T to C mutation

6.5 years ago by

United States

Varun Gupta • 1.2k wrote:

Hi Everyone,

I have a bed file in the following format

chr7 	29434 	29451 	read 	13
chr7 	61642 	61661 	read 	16
chr7 	99192 	99229 	read 	11
chr7 	115309 	115326 	read 	5
chr7 	134211 	134229 	read 	8
chr7 	216704 	216727 	read 	29
chr7 	289611 	289636 	read 	6
chr7 	348415 	348440 	read 	5
chr7 	385948 	385968 	read 	7
chr7 	395913 	396002 	read 	533

These coordinates represent clusters and 5th column represents number of reads in each cluster.

When I view these coordinates one by one on IGV, I noticed that by default the allele frequency threshold is 0.2(which is exactly what i need)

I want to keep only those clusters in which at a position if ref is T (5'--->3') then, in the reads within cluster, it is C such that allele frequency threshold of 0.2 is satisfied.

Similarly for the reads which are mapping to the reverse strand, ref is A and read has G such that at that position allele frequency of 20 % is satisfied.

Is there a way to do that?

Is this possible to do with samtools??

Thanks for the help and time.

Regards
Varun

mutation bed • 1.7k views

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modified 6.5 years ago by EagleEye ♦ 6.7k • written 6.5 years ago by Varun Gupta • 1.2k

6.5 years ago by

Devon Ryan ♦ 98k

Freiburg, Germany

Devon Ryan ♦ 98k wrote:

You'll need to write a program to do that. Using a pileup in pysam or the samtools C API might be the easiest method.

ADD COMMENT • link written 6.5 years ago by Devon Ryan ♦ 98k

Hi Devon,

Anything similar in PERL? Haven't done much coding in python or C. Looking into pysam though.

ADD REPLY • link written 6.5 years ago by Varun Gupta • 1.2k

Probably, I try to stay away from perl, though, so I wouldn't know off-hand.

ADD REPLY • link written 6.5 years ago by Devon Ryan ♦ 98k

6.5 years ago by

EagleEye ♦ 6.7k

Sweden

EagleEye ♦ 6.7k wrote:

Hello Varun,

I have made a PERL script which draws the result from output of VCF file (V4) generated by Freebayes. Please let me know whether you wanted the result like this. I will be soon depositing my scripts into GitHub. Please let me know if you need it and I will update you with the link whenever I am done with structuring my scripts.

This is the script.

https://github.com/santhilalsubhash/TransExtract_betaV1.2.git

But this one is not well structured (you might find it difficult to understand) as I said.

/santhilal

ADD COMMENT • link modified 6.5 years ago • written 6.5 years ago by EagleEye ♦ 6.7k

Hi Santilal,

This looks nice. From the bed file I posted as of now I am only interested in those clusters which have T--> C mutation at a particular locus >= 0.2. I used bowtie with 1 mismatch option so the reads can either have 0 mismatch or 1 mismatch at max.

SO FROM THE ABOVE BED FILE lets say only these many clusters had T-->C mutation >= 0.2. I just want to keep them. Having a nice graph is always good.

chr7 29434 29451 read 13 chr7 61642 61661 read 16 chr7 134211 134229 read 8 chr7 216704 216727 read 29 chr7 395913 396002 read 533

Can you share the perl script??

Thanks

Varun

ADD REPLY • link modified 6.5 years ago • written 6.5 years ago by Varun Gupta • 1.2k

This is the script.

https://github.com/santhilalsubhash/TransExtract_betaV1.2.git

But this one is not well structured (you might find it difficult to understand) as I said.

ADD REPLY • link modified 6.5 years ago • written 6.5 years ago by EagleEye ♦ 6.7k

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