User: serpalma.v

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serpalma.v40
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Germany
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3 months, 1 week ago
Joined:
6 years, 11 months ago
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Posts by serpalma.v

<prev • 85 results • page 1 of 9 • next >
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Evaluating RMSMappingQuality profile to set threshold
... Hello! I am trying to set a threshold to filter my VCF file by using, among other INFO-annotations, RMSMappingQuality (I am using the GATK best practices workflow). According to GATK, a reasonable cutoff value for this annotation is >=50, however, given the RMSMappingQuality profile in my data, ...
variant calling gatk snp filtering written 4 months ago by serpalma.v40 • updated 4 months ago by Nicolas Rosewick9.2k
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Comment: C: Insert size 350bp vs 400bp, any major downstream difference?
... I also though so too, I am doing SNP discovery ...
written 6 months ago by serpalma.v40
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Insert size 350bp vs 400bp, any major downstream difference?
... Hello! I have two data sets one from HiSeq4000 with an insert size of 350bp and another set of reads from NovaSeq with average 400bp. I am wondering if I should have any reasons to belive there would be major consequences of this difference down the line. Both sets of reads have the same length (1 ...
alignment snp sequencing written 6 months ago by serpalma.v40
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how can I extract intervals from bed file spanning a max larger interval in a windowed mode without disrupting intervals?
... Hello! Given this bed file: 1 101 300 1 500 800 1 801 895 1 1001 1250 1 1350 2000 1 2200 2350 1 2500 2700 I would like to separate it into chunks of max 900bp without disrupting intervals. According to the example, that would b ...
bedtools bed bedops sequencing written 6 months ago by serpalma.v40
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Comment: C: How to extract intervals for regions that are masked?
... It does not give the intervals of the regions that are not masked. That is what I really need. ...
written 6 months ago by serpalma.v40
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How to extract intervals for regions that are masked?
... Hello I want to determine the begining and end of each interval formed only by Ns (masked region). Then I would like to split the chromosome into smaller intervals to keep the regions that are not masked. For example: AGGTCGTTNNNNAACTGNNAGTC I would like to get three intervals from this sequenc ...
assembly snp sequencing written 6 months ago by serpalma.v40
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Comment: C: Are there any issues with using sample reads coming from different technologies
... yes, we just got the new data ...
written 8 months ago by serpalma.v40
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Comment: C: Are there any issues with using sample reads coming from different technologies
... We did not add samples from the last batch into the new batch ...
written 8 months ago by serpalma.v40
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Are there any issues with using sample reads coming from different technologies and having different depths to do joint variant calling (gatk)?
... Hello! We are analyzing a WGS data of 60 samples (6 groups, 10 samples/group) produced by HiSeq4000. The mean coverage per sample is 25x (lowest sample is 15x). Now we realized we need to sequence more samples in order to better estimate the allele frequencies. Due to budget and technical constrai ...
variant calling gatk hiseq snp novaseq written 8 months ago by serpalma.v40 • updated 8 months ago by bari.ballew230
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How to replicate vcftool's sliding window SNP density?
... Hello! vcftools can calculate statistics such as pi and Fst using sliding windows. I've noticed that windows in which the alternative allele is fixed are not taken into account. However, those appear in the VCF file. For example, ``N_VARIANTS`` for pi at window_x is 20, but the region in the vcf ...
vcftools snp sequencing written 13 months ago by serpalma.v40 • updated 13 months ago by Vitis2.4k

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