An R-based bioinformatic pipeline to determine killer-cell immunoglobulin-like receptor (KIR) copy number and high-resolution genotypes from short-read sequencing data.
I used WGS and WES data to do PING and it returned with partial results:
Generating SNP tables for IP02_R: KIR2DL1 KIR2DL2 KIR2DL3 KIR2DL4 KIR2DL5 KIR2DP1 KIR2DS2 KIR2DS3-- fewer than 10 aligned reads, skipping --
KIR2DS4 KIR3DL1 KIR3DL2 KIR3DL3 KIR3DP1 KIR3DS1
----- Finished with alignment! -----
finalAlleleCalls.csv and manualCopyNumberFrame.csv are NOT found in the output directory. (I also run the test data and there is no warnings or other errors) Is it because I used whole genome data? But I found your paper published on 2016, in which WES or WGS data was used. Do you have any idea to fix this problem? Thanks.
I used WGS and WES data to do PING and it returned with partial results:
Generating SNP tables for IP02_R: KIR2DL1 KIR2DL2 KIR2DL3 KIR2DL4 KIR2DL5 KIR2DP1 KIR2DS2 KIR2DS3-- fewer than 10 aligned reads, skipping -- KIR2DS4 KIR3DL1 KIR3DL2 KIR3DL3 KIR3DP1 KIR3DS1
----- Finished with alignment! -----
finalAlleleCalls.csv and manualCopyNumberFrame.csv are NOT found in the output directory. (I also run the test data and there is no warnings or other errors) Is it because I used whole genome data? But I found your paper published on 2016, in which WES or WGS data was used. Do you have any idea to fix this problem? Thanks.