Copy consensus sequence from many chromosomes at once
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Ales Bucek
Dec 17, 2017, 11:00:08 PM12/17/17
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I'm wondering if there is a way how to copy consensus sequence from many chromosomes at once?
I can select chromosome one by one and for each of them right click to "Copy consensus sequence", however since I'd like to get the consensus for hundreds of "chromosomes" (in my case actually genes which I used as reference for construction of my bam file) it is not feasible to perform it manually "chromosome-by-chromosome".
The "copy consensus sequence" functionality implemented in IGV is, I believe, quite unique as it reports the type of consensus which might be otherwise impossible (or complicated) to retrieve by other tools for extracting consensus from bam files (e.g. I failed to fine-tune the criteria for extracting consensus using combination of samtools mpileup, bcftools and vcfutils which is typically used to get the consensus). Therefore I believe it would be cool if there is an option (or possibly trick/workaround) how to copy in IGV consensus for many "chromosomes" at once.
Thanks for any hints.
I can select chromosome one by one and for each of them right click to "Copy consensus sequence", however since I'd like to get the consensus for hundreds of "chromosomes" (in my case actually genes which I used as reference for construction of my bam file) it is not feasible to perform it manually "chromosome-by-chromosome".
The "copy consensus sequence" functionality implemented in IGV is, I believe, quite unique as it reports the type of consensus which might be otherwise impossible (or complicated) to retrieve by other tools for extracting consensus from bam files (e.g. I failed to fine-tune the criteria for extracting consensus using combination of samtools mpileup, bcftools and vcfutils which is typically used to get the consensus). Therefore I believe it would be cool if there is an option (or possibly trick/workaround) how to copy in IGV consensus for many "chromosomes" at once.
Thanks for any hints.
Ales Bucek
Jan 21, 2018, 10:55:56 PM1/21/18
to igv-help
Hi,
no hints for this question? I'm aware that IGV was not design for such a task but IGV is giving exactly the consensus I need - the IGV consensus does not include any bases from the reference (e.g. at the positions of low-coverage or ambiguous mapped bases) - this is an output which I'm not able to obtain with the more traditional tools for extracting the consensus such as by combination of samtools and bcftools. Thanks for any hints!
Best,
Ales
no hints for this question? I'm aware that IGV was not design for such a task but IGV is giving exactly the consensus I need - the IGV consensus does not include any bases from the reference (e.g. at the positions of low-coverage or ambiguous mapped bases) - this is an output which I'm not able to obtain with the more traditional tools for extracting the consensus such as by combination of samtools and bcftools. Thanks for any hints!
Best,
Ales
James Robinson
Jan 23, 2018, 4:45:42 PM1/23/18
to igv-help
Hi, there is no way to do this in IGV. I'm surprised there isn't an analysis tool that can do it. If you would like to request this feature please open a git issue, this is probably more appropriate for igvtools (the command line program). You can open a git issue here: https://github.com/igvteam/igv/issues
Apologies for the delayed response.
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James Robinson
Jan 28, 2018, 12:29:11 AM1/28/18
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Hi Ales, I'm exploring the possibility of adding this to igvtools. How do you envision the input and output?
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