Hello, I'm sorry but I can't seem to find this information in the manual. Can you tell me what the flag sb_holmbonf means in the output vcf? I have a lot of SNPs with this flag. Thanks!
these are SNVs that show significant strand bias (sb) and are therefore
filtered. Corresponding pvalues were corrected using the Holm Bonferroni
method (holmbonf). This is the default setting. The vcf header should
contain one line entry describing this. It's also briefly mentioned in the
2012 LoFreq paper.
Hello, I'm sorry but I can't seem to find this information in the manual.
Can you tell me what the flag sb_holmbonf means in the output vcf? I have a
lot of SNPs with this flag. Thanks!
Hello, I'm sorry but I can't seem to find this information in the manual. Can you tell me what the flag sb_holmbonf means in the output vcf? I have a lot of SNPs with this flag. Thanks!
eg
sb_holmbonf DP=8333;AF=0.009720;SB=179;DP4=4220,3897,78,3
Hi Jessica,
these are SNVs that show significant strand bias (sb) and are therefore
filtered. Corresponding pvalues were corrected using the Holm Bonferroni
method (holmbonf). This is the default setting. The vcf header should
contain one line entry describing this. It's also briefly mentioned in the
2012 LoFreq paper.
Andreas
On 17 Sep 2015 02:37, "jessica preston" jpreston555@users.sf.net wrote: