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typing additional loci #20

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afadda91 opened this issue Nov 19, 2018 · 19 comments
Open

typing additional loci #20

afadda91 opened this issue Nov 19, 2018 · 19 comments

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@afadda91
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hi,
when i use the -a option it only types A,B,C,DQA1,DRB1. if i specify -a MICA for instance, i get the message "Input bam : A DOES NOT exist. Please check the bam exists." I know the MICA reads are present in the KouramiPanel.bam. So what is the problem.
Also, is there an explanation to the numbers that come in the results file ?

thanks
@heewookl
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The bam does not exist error has nothing to do with -a flag. Could you please provide the entire command line you used to run Kourami?

-a flag does not take any value. -a flag just triggers Kourami to type pre-defined additional loci: DOA DMA DMB DPA1 DPB1 DRA DRB3 DRB5 F H J L

MICA locus is currently not supported.

@afadda91
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afadda91 commented Nov 20, 2018 via email

@heewookl
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As I explained earlier '-a' flag doesn't take any value, that's why you are getting the error "A DOES NOT exist as the command-line option parser is assuming 'A' is one of input bam files.

The reason you are only getting A,B,C, DQA1, and DRB1 (Not DQB1) is probably due to an insufficient amount of sequence coverage. Are you running Kourami on whole-genome sequencing data? If so, do you know what is the average sequencing depth?

Could you also copy and paste the content of the output file ending with ".result" ? Thanks!

@afadda91
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afadda91 commented Nov 21, 2018 via email

@heewookl
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Could you please either copy and paste the content of the file instead of attaching the file to email? Thanks.

@afadda91
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afadda91 commented Nov 21, 2018 via email

@heewookl
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They are explained in README: https://github.com/Kingsford-Group/kourami/blob/master/README.md

Last 3 columns which are depths related number and they look pretty small for 30X.

Which flavor of human reference genome did you use when you initially generated bam alignment of all WGS reads?

@afadda91
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afadda91 commented Nov 21, 2018 via email

@afadda91
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afadda91 commented Nov 21, 2018 via email

@heewookl
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So did you realign the entire 30x coverage of WGS to hs38HD?

Could you please run the following 2 commands? thanks!
<initial_bam> is the baffle of the entire WGS mapped to hs38DH NOT to kourami panel.

samtools view -H <initial_bam>
samtools view -c <initial_bam>

@afadda91
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afadda91 commented Nov 28, 2018 via email

@heewookl
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Thanks for providing the header for the bam. I think the message may have gotten truncated because of the length. Could you also provide the output for -c flag? Thanks!

samtools view -c <initial_bam>

@afadda91
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afadda91 commented Nov 29, 2018 via email

@afadda91
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afadda91 commented Dec 17, 2018 via email

@afadda91
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afadda91 commented Feb 28, 2019 via email •
edited by heewookl
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@heewookl
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heewookl commented Mar 1, 2019

Hi,

I will try to take a look at it next week. Would it be possible for you to share one of the bam files that you had trouble with? This will help me when I try to figure why some genes were not getting assembled. Thank you.

@afadda91
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afadda91 commented Mar 4, 2019 via email

@freshfischer
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freshfischer commented Aug 27, 2020 •
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hi,
when i use the -a option it only types A,B,C,DQA1,DRB1. if i specify -a MICA for instance, i get the message "Input bam : A DOES NOT exist. Please check the bam exists." I know the MICA reads are present in the KouramiPanel.bam. So what is the problem.
Also, is there an explanation to the numbers that come in the results file ?

thanks

-a option seems to caculate and output all the loci that aligned to hg38 reference and IMGT/IPD HLA database. code as follow:
$kourami/scripts/alignAndExtract_hs38DH_NoAlt.sh -d $kourami/custom_db/3.40.0/ -r $kourami/resource $sample $inbam

java -jar $kourami/build/Kourami.jar -d $kourami/custom_db/3.40.0/ -a -o $sample ${sample}_on_KouramiPanel.bam

@prmac
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prmac commented Dec 11, 2020

The bam does not exist error has nothing to do with -a flag. Could you please provide the entire command line you used to run Kourami?

-a flag does not take any value. -a flag just triggers Kourami to type pre-defined additional loci: DOA DMA DMB DPA1 DPB1 DRA DRB3 DRB5 F H J L

MICA locus is currently not supported.

Is MICA supported now?

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@heewookl @prmac @afadda91 @freshfischer