User: ravi.uhdnis

gravatar for ravi.uhdnis
ravi.uhdnis170
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170
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United States
Last seen:
2 years ago
Joined:
4 years, 10 months ago
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r**********@gmail.com

Posts by ravi.uhdnis

<prev • 65 results • page 1 of 7 • next >
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Why only False Positives after VQSR ist step ?. Variant Annotation Software for combined g.vcf file !!
... Hi all, I am working with Human sample WGS data (30X, PE reads, HiSeq platform) and facing problem at VQSR and variant annotation step. I ran following commands (modified here, path deleted) to get my files, please see my 2 questions after these commands: Converted each sample's bam file into gVCF ...
genome assembly next-gen snp sequencing written 3.1 years ago by ravi.uhdnis170 • updated 22 months ago by RamRS25k
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Comment: A: GATK IndelRealigner issue "TOO MANY READS"
... A nice explanation of this issue is given at this link: http://gatkforums.broadinstitute.org/gatk/discussion/3292/indelrealigner-not-attempting-realignment-in-interval ...
written 3.5 years ago by ravi.uhdnis170
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Comment: C: 'make' command repeated message while installing vcftools on Ubuntu 14.04 LTS.
... Ah...I got it !! I need to write in .bashrc and source it rather than in .bash_profile. I tried with plink as PATH=$PATH:/home/rsindhu/ngSoftwares/PLINK/plink-1.07-x86_64 , export PATH ; source .bashrc and it worked !!. ...
written 3.8 years ago by ravi.uhdnis170
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Comment: C: 'make' command repeated message while installing vcftools on Ubuntu 14.04 LTS.
... I guess so, now since it is successfully installed it is showing as which vcftools => /usr/bin/vcftools. Also, similar other packages (samtools, bcftools) also installed in /usr/bin. It means nothing is placed in my class path, i installed them using apt-get install long before and forget their o ...
written 3.8 years ago by ravi.uhdnis170
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Comment: C: 'make' command repeated message while installing vcftools on Ubuntu 14.04 LTS.
... a little incorrect comment by me (above), i put vcftools in my in .bash_profile file without any issue, sourced it but it didn't worked (vcftools)....like many others e.g. bcftools, samtools in the path. PATH=$PATH:/home/rsindhu/ngSoftwares/vcftools-vcftools-678e892/cpp export PATH even tried /bin ...
written 3.8 years ago by ravi.uhdnis170
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Comment: C: 'make' command repeated message while installing vcftools on Ubuntu 14.04 LTS.
... I think one can install vcftools by either of these two ways. The way you told me, i was able to install it but couldn't put in my PATH. Therefore, i tried the other way and apt-get install command made my job done. thanks for comments. ...
written 3.8 years ago by ravi.uhdnis170
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Comment: C: 'make' command repeated message while installing vcftools on Ubuntu 14.04 LTS.
... thanks for the information. the only problem was the connectivity to internet while using apt-get command earlier, since it is working now..it's best way to install any software by this way. ...
written 3.8 years ago by ravi.uhdnis170
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Comment: C: 'make' command repeated message while installing vcftools on Ubuntu 14.04 LTS.
... I downloaded vcftools (vcftools-master.zip) from Github (https://github.com/vcftools/vcftools), unzipped it to make vcftools-master folder. There were following files in it : drwxrwxr-x 4 rsindhu rsindhu 4096 May 5 2016 src -rw-rw-r-- 1 rsindhu rsindhu 1928 May 5 2016 README.md -rw-rw-r-- 1 rsin ...
written 3.8 years ago by ravi.uhdnis170
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Comment: C: 'make' command repeated message while installing vcftools on Ubuntu 14.04 LTS.
... because i knew that FTP proxy permission were blocked for my system BUT i tried your suggestion and it worked !! Surely, proxy permission are changed now as earlier it always gave error of internet connectivity. Lesson for today, always try the simplest ist. Thank you Ram. ...
written 3.8 years ago by ravi.uhdnis170
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'make' command repeated message while installing vcftools on Ubuntu 14.04 LTS.
... Hi, I downloaded vcftools (vcftools-master.zip), unzipped it to make vcftools-master, then run following commands in it: ``` ./autogen.sh ./configure make ``` but, the make output is repeatedly giving following message: ``` ******************************************* /bin/bash ./config.status -- ...
software error written 3.8 years ago by ravi.uhdnis170 • updated 3.8 years ago by RamRS25k

Latest awards to ravi.uhdnis

Great Question 2.4 years ago, created a question with more than 5,000 views. For Marking and Removing duplicates using picard (picard-tools-1.129)
Epic Question 2.9 years ago, created a question with more than 10,000 views. For Marking and Removing duplicates using picard (picard-tools-1.129)
Epic Question 2.9 years ago, created a question with more than 10,000 views. For Running and Analyzing fastqc on multiple fastq files
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Methods to count Number of SNPs and Novel SNPs in a Variant Calling File (.vcf) ?.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For GATK IndelRealigner issue "TOO MANY READS"
Student 2.9 years ago, asked a question with at least 3 up-votes. For Error while running BWA mem
Great Question 3.0 years ago, created a question with more than 5,000 views. For Marking and Removing duplicates using picard (picard-tools-1.129)
Great Question 3.4 years ago, created a question with more than 5,000 views. For Running and Analyzing fastqc on multiple fastq files
Great Question 3.6 years ago, created a question with more than 5,000 views. For Marking and Removing duplicates using picard (picard-tools-1.129)
Popular Question 3.9 years ago, created a question with more than 1,000 views. For samtools (conversion from .sam to .bam) and sorting of .bam file
Popular Question 4.1 years ago, created a question with more than 1,000 views. For samtools (conversion from .sam to .bam) and sorting of .bam file
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Marking and Removing duplicates using picard (picard-tools-1.129)
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Running and Analyzing fastqc on multiple fastq files
Supporter 4.7 years ago, voted at least 25 times.

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