tyyiyi

the flag of bam

1

Hello, I am currently doing structural mutation detection. One of the steps is to filter out discordant reads based on the flag value in the bam file. The script is...

Hello, I am using smoove to call SV. Some of the information in the output file it produces makes me confused. I asked brentp and he told me that the...

targeted sequencing call SV

3

Hi, I am using smoove to call SVs. I have about 50 samples, which are tumor-normal pairs of human. Their sequencing depth is about 1000X, which is targeted sequencing. I...

I am testing structural variations on my samples, and their depth is about 1000x. I tested a pair of normal tumor samples,using sorted.bam and markduplicates.bam as input files respectively, the...

excluding variants with all unknown or homozygous reference genotypes

2

Command line: $smoove call --outdir $smooveout --name ${tumor}_${normal} --fasta $ref -p 1 --genotype $tdata/$tumor.MarkDuplicates.bam $ndata/$normal.MarkDuplicates.bam error: [smoove] 2020/07/16 16:40:21 starting with version 0.2.3 [smoove] 2020/07/16 16:40:21 calculating bam stats for...

How to distinguish between INV and BND

1

Hi, I am using smoove to call SVs. I want to know why some mutations in the chromosome are INV and some are BND. There are some results, for example:...

I intend to detect structural variation in UMI data, So want to use gencore to process the raw data,so,could you please elaborate on how gencore deals with split reads and...

target sequencing?

4

Hi, I am using lumpy express to call SVs. I have about 60 samples, which are tumor-normal pairs of human. Their sequencing depth is about 1000X, which is targeted sequencing....

Hi, I want to go to the Google forum to ask some questions, however, when I go to https://groups.google.com/forum/#!forum/lumpy-discuss, it reminds me: "This group does not exist, or you have...