User: amitgsir

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amitgsir50
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Location:
Incheon, South Korea
Last seen:
2 years, 1 month ago
Joined:
4 years, 1 month ago
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a*******@pusan.ac.kr

Posts by amitgsir

<prev • 11 results • page 1 of 2 • next >
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Comment: C: CONTRA for CNV detection. troubleshooting
... Great~~worked for me. But changing thr --minExom provides the diffrent values in *.CNATable.10rd.10bases.20bins.txt file. Is it okay? ...
written 2.2 years ago by amitgsir50
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Comment: C: GC-BIAS correction for BAM file
... Yeah, Fixing the seed using np.random.seed(1234) is giving the exact same results each time. Thanks ...
written 3.2 years ago by amitgsir50
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Comment: C: GC-BIAS correction for BAM file
... Thanks Ryan, I will try this and will inform you if this works. ...
written 3.2 years ago by amitgsir50
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GC-BIAS correction for BAM file
... Hi, I am looking for any software which can correct the GC-Bias in the BAM file and provides the output as BAM. I know that deeptools (correctGCBias) does the exactly same job, but the output of the deeptools is variable in each run. So, I am looking for more specific tool. Basically, I want t ...
genome R rna-seq deeptools written 3.2 years ago by amitgsir50 • updated 3.2 years ago by Biostar ♦♦ 20
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Comment: C: Compare two vcf like files; and output the line for unique position (from first
... Thanks Sean for the suggestions~~!! I tried some awk combination and able to get the output. ...
written 3.5 years ago by amitgsir50
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Comment: C: Compare two vcf like files; and output the line for unique position (from first
... Hi Sean, This is working for the small text file but running continuously for large file (~1million lines in both files) and throwing no result. Also, I it is only providing the uniq line from the File1.txt while I want to keep Match positions line from File2.txt as well in output file.   Thanks ...
written 3.5 years ago by amitgsir50
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Compare two vcf like files; and output the line for unique position (from first file) and line for duplicate position (from second file)
... I have two tab separated values file, say File1.txt chr1 894573 rs13303010 GG chr2 18674 rs10195681 CC chr3 104972 rs990284 AA <--- Unique Line chr4 111487 rs17802159 AA chr5 200868 rs4956994 **GG** chr5 303686 rs6896163 AA <--- Unique Line chrX 33103 ...
vcf written 3.5 years ago by amitgsir50 • updated 3.5 years ago by Sean Davis25k
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Answer: A: Convert annovar file to vcf file
... I got an answer for Kai Wang. I hope it can help others too.   "Hi Amit, You will need to convert this to VCF yourself, by padding the nucleotide that corresponds to "-". This can be done by retrieve_seq_from_fasta.pl (specifying chr:start-end).   But you can certainly compare this file to VCF ...
written 4.1 years ago by amitgsir50
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Comment: C: Finding Overlapping Variants (I.E. Indels, Snps) Using Annovar Format.
... Hi Young, Could you find any tool which could use annovar format to find the overlapps. Thanks, Amit ...
written 4.2 years ago by amitgsir50
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Comment: C: How To Prepare Gatk .Vcf Files Output For Annovar ?
... Also, is there any way to convert the Annovar file (containing INDELs info) to vcf file (using hg19 as ref genome). ...
written 4.2 years ago by amitgsir50

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Convert annovar file to vcf file

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