User: Sandeep

gravatar for Sandeep
Sandeep250
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250
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Location:
Manipal, India
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10 hours ago
Joined:
7 years, 1 month ago
Email:
p*************@gmail.com

Posts by Sandeep

<prev • 84 results • page 1 of 9 • next >
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... I think I figured out the problem. I went back to bed file to inspect it near the region samtools exits. There seems to be a blank line separating two entries. chr7 100893945 100894175 ACHE_80133.3.2392 0 + . GENE_ID=ACHE;Pool=10;TRIM_LEFT=0;TRIM_RIGHT=0 chr7 100894084 100894305 ACHE_80133 ...
written 25 days ago by Sandeep250
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... The last cordinate on chr7 in my bam is 0IN8L:03162:11340 16 chr7 159335889 0 34M * 0 0 ...
written 25 days ago by Sandeep250
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... tail sample_merged.sorted.mpileup on two different machines have given me identical output. chr7 100894296 A 50 ,................,,,,,,,,,,,,,,,,,,.,,,,,,,.,,.,,, @47362967899964:7<>7>>9<>;?B9<4:7< 33 .........,,,,,,,,,,,,,,,,,.,,..,, 086474599;<;<;>=B< ...
written 25 days ago by Sandeep250
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... Now this is frustrating. Even after cleaning the headers, I am having the same issue. $ cut -f 1 sample_merged.sorted.mpileup | uniq chr1 chr2 chr3 chr4 chr5 chr6 chr7 I am stumped. Not really sure how to proceed from here. ...
written 25 days ago by Sandeep250
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... I used samtools merge samtools merge -@ 32 Normal_merged.bam Normal1.bam Normal2.bam Normal3.bam My reference file also had non standard chromosomes in them. SN:chr11_KI270721v1_random SN:chr14_GL000009v2_random SN:chr14_GL000225v1_random SN:chr14_KI270722v1_random SN:chr ...
written 25 days ago by Sandeep250
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... Update: quickcheck executed without errors. I tried resorting the bam and ran mpileup. I also tried running mpileup on another machine. All of the steps have generated only an incomplete pileup file. It is confirmed something is going wrong with mpileup step. I have posted the issue on github, let m ...
written 26 days ago by Sandeep250
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... Thanks for the suggestion. I am currently re-sorting the merged bams. Will update this thread once done. ...
written 4 weeks ago by Sandeep250
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... Seems like I figured out where the problem lies. I just did a grep on the mpileup file. grep 'chr1' normal-tumor.mpileup chr1 68929 A 88 ..............,..............................................,,,,,,,,,,,,,,,,,,,,,,,,,,^!. ><588=<7>?;948/>===<<;<=@<;=@? ...
written 4 weeks ago by Sandeep250
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... wc -l on the output vcf files shows approximately 18k each. That makes it a total of 36k polymorphisms called. The log file has more than 58k polymorphisms called. I have separately generated mpileup file and run the analysis. Same output. Currently, I am running the same on Varscan v.2.4.2 to chec ...
written 4 weeks ago by Sandeep250
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Comment: C: VarScan.v2.4.3 generating incomplete or partial VCF file
... Thanks for the reply. I just reconfirmed again by opening Ampliseq file. It contains all chromosomes. Infact, the log files has total number of variants called but the saved vcf files do not have them. ...
written 4 weeks ago by Sandeep250

Latest awards to Sandeep

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Popular Question 3.4 years ago, created a question with more than 1,000 views. For Align short reads to multiple reference sequence
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Popular Question 4.6 years ago, created a question with more than 1,000 views. For Which Tool Is Used To Plot The Ideogram Shown Here?
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