User: Inquisitive8995

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Posts by Inquisitive8995

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Comment: C: VCF tools --freq output file
... Thank you. I suppose I can use, > bcftools view --max-alleles 2 for retaining positions with only 2 alleles. Then, I will try awk and obtain just the minor allele frequency. ...
written 27 days ago by Inquisitive8995170
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Comment: C: VCF tools --freq output file
... Hi, Thanks for your reply. If I go by the calculation, can I confidently say that the first column is MAF for creating a MAF plot. What would I infer from a SNP having three alleles as seen in contig_3:277244. Do have any suggestions about it ? Thank u ...
written 27 days ago by Inquisitive8995170
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VCF tools --freq output file
... Hello, I am using VCFTools --freq to obtain allele frequencies of my VCF file consisting of 4 individuals. I used the below command to run vcftools --vcf A.vcf --freq --out A.frq My output file looks like below: CHROM POS N_ALLELES N_CHR {ALLELE:FREQ} contig_1 ...
vcftools allelefrequency fileformat written 28 days ago by Inquisitive8995170 • updated 27 days ago by Kevin Blighe63k
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Comment: C: Minimap2 giving 2 TB sam file as an output
... Thanks for your reply. Is there anyway with which I can restrict the mapping to only the top hit or something like that ? Are there any parameters in Minimap to do so ? ...
written 8 months ago by Inquisitive8995170
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Comment: C: Minimap2 giving 2 TB sam file as an output
... Noted. Thank you for mentioning this ...
written 8 months ago by Inquisitive8995170
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Comment: C: Minimap2 giving 2 TB sam file as an output
... Thanks for your answer. But I am still confused as the other 2 files of the same size gave the output of around 500Mb and this gives 2TB. ...
written 8 months ago by Inquisitive8995170
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Minimap2 giving 2 TB sam file as an output
... Hello, I have been trying to run Minimap2 with fasta files of ~200Mb. I have 3 such files which I am trying to map onto a reference genome. The output sam file of first 2 files are about 500MB. But the third file gives a 2TB sam file and it has not completed running. Is there any reason of why this ...
minimap2 sequence alignment written 8 months ago by Inquisitive8995170 • updated 8 months ago by h.mon30k
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Comment: C: what do the bcftools ROH output "markers & quality" fields indicate ?
... I am not sure if this is the correct answer but I think I figured out what RG and ST can be. When you use multiple sample VCF file, it calculates ROH over a region (RG) but when you use a single sample VCF file, it gives you the state (ST; either HW or AZ) ...
written 12 months ago by Inquisitive8995170
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what do the bcftools ROH output "markers & quality" fields indicate ?
... Hello all, I understand this is a very basic question but I am unable to find the explanation for the 2 columns in bcftools ROH output. I went through their manual in [https://samtools.github.io/bcftools/howtos/roh-calling.html][1]. But could not find the output format explanation. The header loo ...
roh sequencing written 12 months ago by Inquisitive8995170 • updated 12 months ago by Ximena0
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Comment: C: How to find pattern matching over range of columns but not present in other colu
... Thank you very much @SMK ...
written 13 months ago by Inquisitive8995170

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