User: f1978hp

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f1978hp20
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Posts by f1978hp

<prev • 6 results • page 1 of 1 • next >
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Comment: C: bcftools variant calling query
... Hi Kevin! Thanks for your interesting! The source of the statement is another answer to my query that I was propose later. See the link https://www.biostars.org/p/392106/ There you will undertand the problem better. ...
written 6 months ago by f1978hp20
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bcftools variant calling query
... "During variant calling bcftools compares the average mapping quality of reads supporting a variant with those they don't. If there is a significant difference it will skip this variant. " Are there someone that can explain me how to create a BAM file with the reads that didn't supported the variant ...
next-gen alignment bcftools sequencing written 6 months ago by f1978hp20 • updated 6 months ago by Kevin Blighe55k
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Comment: C: Command line explain
... Thanks fin swimmer! Do you know if there is a way to create a BAM file with these reads that skipped a variant because of a high difference in mapping quality? I would like to know better about this and appreciate a lot if you recommend a bibliography. PS: Sorry about the duplication. ...
written 7 months ago by f1978hp20
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Comment: C: Command line explain
... Hello fin swimmer! But, how bcftools leads to fewer false positive variant calls based on decreasing the mapping quality? For example, if i had a read with excessive mismatches, the parameter -C 50 will decrease your MQ so at what point (argument) in this case bcftools will use the new value of MQ ...
written 7 months ago by f1978hp20
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Command line explain
... I see a command line used to variant calling but i don't understand a particular point. The command line is below. samtools mpileup -C50 -d10000 -L1500 -uf REF_FASTA -I BEDFILE --output-tagsDP,DP4 -r {} Sample.BAM and so, bcftools call -mv > sample.{}.vcf The part that i don't underst ...
bcftools mpileup written 7 months ago by f1978hp20 • updated 7 months ago by finswimmer13k
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-C 50 parameter MPILEUP
... In Samtools documentation are this descrition: -C, --adjust-MQ INT Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sq ...
next-gen sequencing written 8 months ago by f1978hp20 • updated 8 months ago by finswimmer13k

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