User: lebedana21

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lebedana210
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Posts by lebedana21

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Comment: C: find reads information in .vcf file
... Thank you Pierre for response, I had checked all of the tools. However, no seems suitable for my goal. In particular, I need to call all variants (not just a couple, mb my example was confusing, sorry for that), and preserve information about reads for each allele for each variant. For instance, ...
written 8 months ago by lebedana210
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Answer: A: MutScan: Detect important mutations by scanning FastQ files directly
... Hi Chen, I was trying to run the stable releases of MutScan on my data, by executing the following command: `./mutscan -1 my_reads.fq -m my_mutations.csv -S 1` I was expecting to see output for variants, for which at least a single read match the mutation specified in the *my_mutations.csv*. But ...
written 8 months ago by lebedana210
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find reads information in .vcf file
... Hi all, I was wondering if is possible to have reads identification(Id/name) in .vcf file? It might be useful, for instance, when you pick two following variants and want to check how the specific read match the variants? I didn't find any related information in .vcf specification, but still hop ...
.vcf written 8 months ago by lebedana210 • updated 8 months ago by Pierre Lindenbaum112k
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Comment: C: Create small BAM file with pysam and iterate over reads
... Thank Pierre for the link. I finally had used wgsim and obtained the desired .bam file. I followed similar steps as those listed in the post https://www.biostars.org/p/150010/ to generate aligned paired end reads. Executed steps were: ------------------------------ * Manually create small ref ...
written 11 months ago by lebedana210
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Create small BAM file with pysam and iterate over reads
... I was trying to create a small .bam file with pysam (really small, to debug my code). I did succeed by copping header from another file and inserting couple of manually created reads. However, I was not able to iterate over reads in the file with samfile.fetch() ether similar iterators specifying po ...
samtool bam pysam written 11 months ago by lebedana210

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