cauyrd
commented
6 years ago .mapping.indel.vcf contains the indels that are from split read realignment. .assembly,inde,vcf contains the large novel sequence insertions that are inferred using de novo assembly strategy.
.merged.indel.vcf should contained the merged indels from .mapping and .assembly file. If this is an empty file, it suggest there is something wrong with the merging script. But you should have all your predictions from .mapping and *.assembly file.
On Sat, Jun 23, 2018 at 3:31 AM, terra1666 notifications@github.com wrote:
I ran ScanIndel on my data and obtained some outputs. What I'm not very clear about is the VCF files of output. I have 18209 lines for .assembly.indel.vcf and 247 lines for .mapping.indel.vcf. However, there is no line in *.merged.indel.vcf (it is just a empty file with size 0). In such case, what is the reasonable conclusion I should make about indel?
.mapping.indel.vcf .assembly.indel.vcf *.merged.indel.vcf
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I ran ScanIndel on my data and obtained some outputs. What I'm not very clear about is the VCF files of output. I have 18209 lines for .assembly.indel.vcf and 247 lines for .mapping.indel.vcf. However, there is no line in *.merged.indel.vcf (it is just a empty file with size 0). In such case, what is the reasonable conclusion I should make about indel?
.mapping.indel.vcf .assembly.indel.vcf *.merged.indel.vcf