User: shahbazmunir11

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Posts by shahbazmunir11

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Read Vcf file using htsjdk library
... ##fileformat=VCFv4.1 ##source=HANDS2v1.0 ##Genome=1 #CHROM POS ID REF ALT QUAL FILTER INFO Bra1.27 3355 . T . 100 . HSP=K;FC=Y;DB=T Bra1.27 3527 . G A 100 . HSP=R;FC=Y;DB=G Bra1.27 3538 . A T 100 . HSP=W;FC=Y;DB=A Bra1.27 3543 . T C 100 . HSP=Y;FC=N;DB=* Bra1.27 3 ...
written 2.9 years ago by shahbazmunir1110 • updated 2.9 years ago by Pierre Lindenbaum128k
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Comment: A: Read Vcf file using htsjdk library
... Case1: Sample_Error header 3rd line ##HANDS2CommandLine ...
written 2.9 years ago by shahbazmunir1110 • updated 2.9 years ago by Pierre Lindenbaum128k
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Comment: C: Read Vcf file using htsjdk library
... Case 1: The file "Sample2_Working" is working but the file "Sample_Error" gives an error. Both files are same but with the different header. Case 2: The file "Sample2_Working" is working but with another error. "An index is required, but none found". How can I generate the index file? Thanks ...
written 2.9 years ago by shahbazmunir1110
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Read Vcf file using htsjdk library
... Hi, I am using htsjdk library and want to read vcf file. I tried the following code but it gives error "Exception in thread "main" htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VC ...
ngs written 2.9 years ago by shahbazmunir1110
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Comment: C: Print header of bam file using htsjdk library
... Thanks... it worked ...
written 2.9 years ago by shahbazmunir1110
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Print header of bam file using htsjdk library
... Hi, I am using htsjdk library and want to print the header of bam file. I tried but the following code just prints the first header line again and again. I want all header lines. Any suggestions?? Thanks for your time and consideration. File bamFile =new File("SampleFile.bam"); SamRead ...
ngs samformat written 2.9 years ago by shahbazmunir1110 • updated 2.9 years ago by Pierre Lindenbaum128k
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Multi-SNP haplotypes in GWAS data
... ​Hi, I have coordinates in bed format and i am interested to associate SNP with the segments. I looked at plink format but here data is in tsv format. I tried to convert tsv format to bed format but there are multi-SNP haplotypes or SNP-SNP interactions. (Here is sample file link) "[GWAS Sample File ...
gwas snp written 3.5 years ago by shahbazmunir1110
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(Closed) Process GWAS data?
... Hi, i want to process GWAS data which is in tsv format. I have some coordinates in bed format and i am interested to search those coordinates in GWAS data. Is there any tool which perform such kind of tasks? Any suggestion?? Thanks for your consideration. ...
gwas next-gen written 3.5 years ago by shahbazmunir1110 • updated 3.5 years ago by Ron990
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Blastn for Short Sequences
... Hi, i want to do Blastn for short sequences. e.g sequence with length of 11 nuclteotides. Here is the sample. test.fa >Query_1 TGTTCAGCACT $ blastn -db anyGenome -query test.fa -task "blastn-short" -output test_Output -outfmt 7 -word_size 7 -dust yes -evalue 1000 -ungapped B ...
alignment next-gen tool blast written 3.8 years ago by shahbazmunir1110 • updated 3.8 years ago by genomax83k
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Comment: C: I want to Parse Blastn output file which is in Pairwise alignment format and get
... Thanks I find solution using xml output format. ...
written 4.0 years ago by shahbazmunir1110

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Popular Question 23 months ago, created a question with more than 1,000 views. For install UCSC liftover utility from source code
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Popular Question 2.3 years ago, created a question with more than 1,000 views. For Blastn for Short Sequences

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