User: vaibhash

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vaibhash0
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Posts by vaibhash

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Comment: C: How to confirm if VCF file is normalized and Left aligned ?
... lib/utils.c file doesn't exists in the lib folder ... https://github.com/atks/vt/tree/master/lib/libdeflate/lib which we refer in the Makefile of libdeflate LIB_SRC := lib/deflate_decompress.c lib/utils.c \ $(wildcard lib/*/cpu_features.c) and we get the following error while building ...
written 2 days ago by vaibhash0
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Comment: C: How to confirm if VCF file is normalized and Left aligned ?
... I guess its more about "control" than any other reason ... I will ask if vt can be installed, and also if mini-condo can be installed... but I'm very surprised with the issue with vt ... I checked the current version of code on GitHub and they are calling make for a file that doesn't exists in the ...
written 2 days ago by vaibhash0
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Comment: C: How to confirm if VCF file is normalized and Left aligned ?
... Thanks dariober for the comment ... I didn't even attempt to run conda as our admin says ... "We request our users to please not install Anaconda on the clusters" I started the normalization step via bcftools ... it takes care of the decomposition scenario, will surely try out the vt tool when issu ...
written 2 days ago by vaibhash0
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Comment: C: How to confirm if VCF file is normalized and Left aligned ?
... Thanks again @ _r_am I see your point about adding reply or comment !!! will be more cautious next time ... its a cluster and sysadmin doesn't allow usage of Conda ... ...
written 3 days ago by vaibhash0
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Comment: A: How to confirm if VCF file is normalized and Left aligned ?
... Thanks @_r_ram for your enlightening response, much appreciated ... tried installing the vt tool but seeing this error : https://github.com/atks/vt/issues/113 can't use Conda in my enviornment .. :( But then what is life without some struggle ? :D ...
written 3 days ago by vaibhash0
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How to confirm if VCF file is normalized and Left aligned ?
... Hi Team, As I'm a newbie my question might be very lame, so please bear with me ... I was told that if we find a multi-allelic entry in our VCF file than it means that it is not normalized, and thus left-aligned ? ( multiple values under ALT column , in our case **T,A** and **A,T**) I found belo ...
vcf normalization alignment bcftools ukbb written 3 days ago by vaibhash0
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Answer: A: variant filtering based on high quality reference - removing false positives
... @4galaxy77 oh my wonderful friend ... much love and respect to you !!! may the force be with you ... forever and ever !!! I will try this approach and revert back if any further question .... much thanks !!! ...
written 13 days ago by vaibhash0
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variant filtering based on high quality reference - removing false positives
... Hello Wonderful people !!! I'm new to the world of bio-informatics and this is my first post, so please forgive me for any unintended mistake ... The VCF file that I'm working on are missing ##INFO variables like QD, FS, SOR, MQ, MQRankSum, ReadPosRankSUm, InbreedingCoeff ... may be one can gener ...
genome vcf sequence variant quality control written 13 days ago by vaibhash0

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