The output I got were:
FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput.hg19_multianno.txt
FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput.invalid_input
FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput.wgEncodeGencodeBasicV19.invalid_input
I have number 1 (FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput.hg19_multianno.txt)
but I do not have number 2 and 3.
instead they are called "invalid input"
I have also attached the script that was ran in case it would be clear from that what I am missing. I looked through the script but there doesn't appear to be any errors.
If you know how I could fix this and get the correct output, I would really appreciate it! Thanks so much!
Hi, I ran the family_psap_pipeline.sh script
The output I got were: FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput.hg19_multianno.txt FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput.invalid_input FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput.wgEncodeGencodeBasicV19.invalid_input
inside the annotated folder, and
FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput.header
outside of the annotated folder.
According to the PSAP guidelines there should be 3 outputs:
1) FILENAME.avinput.hg19_multianno.txt 2) FILENAME_popScore.txt 3) FILENAME.report.txt
I have number 1 (FAM1_1.avinput.hg19_multianno.fampsap.OUTFILE.avinput.hg19_multianno.txt) but I do not have number 2 and 3. instead they are called "invalid input"
I have also attached the script that was ran in case it would be clear from that what I am missing. I looked through the script but there doesn't appear to be any errors.
If you know how I could fix this and get the correct output, I would really appreciate it! Thanks so much!
M [family_psap_run.txt](https://github.com/awilfert/PSAP-pipeline/files/1031784/family_psap_run.txt)