Not called SNPs in lowercase letter in output FASTA
Your environment
version of jvarkit: dbdbed3a9
version of java: openjdk version "17.0.10" 2024-01-16
the value of ${JAVA_HOME}
Ubuntu 22.04.03 LTS
Steps to reproduce
I wondered whether it would be possible to include an option that indicates in the output FASTA that for a certain SNP that has not been called for a given sample in the vcf (e.g. based on VcfToTable output) a lowercase letter is used, and capital letters are only used for SNPs that have been called/have read coverage. Please find below an example that illustrates my request.
Simplified VcfToTable output for a certain SNP, for 13 samples:
REF A
ALT T Sample Type AD
Sample_1 NO_CALL 0,0
Sample_2 NO_CALL 0,0
Sample_3 NO_CALL 0,0
Sample_4 HOM_REF 1,0
Sample_5 HOM_REF 2,0
Sample_6 NO_CALL 0,0
Sample_7 HOM_REF 2,0
Sample_8 HOM_REF 3,0
Sample_9 HOM_REF 3,0
Sample_10 HOM_VAR 0,2
Sample_11 HOM_REF 2,0
Sample_12 NO_CALL 0,0
Sample_13NO_CALL 0,0
nucleotide representation in Biostar398854 output FASTA for the same SNP for these 13 samples:
Sample current output of Biostar398854 requested output of Biostar398854
Sample_1 a a
Sample_2 a a
Sample_3 a a
Sample_4 a A
Sample_5 a A
Sample_6 a a
Sample_7 a A
Sample_8 a A
Sample_9 a A
Sample_10 T T
Sample_11 a A
Sample_12 a a
Sample_13 a a
Subject of the issue
Not called SNPs in lowercase letter in output FASTA
Your environment
${JAVA_HOME}Steps to reproduce
I wondered whether it would be possible to include an option that indicates in the output FASTA that for a certain SNP that has not been called for a given sample in the vcf (e.g. based on VcfToTable output) a lowercase letter is used, and capital letters are only used for SNPs that have been called/have read coverage. Please find below an example that illustrates my request.
Simplified VcfToTable output for a certain SNP, for 13 samples:
REF A
ALT T
Sample Type AD Sample_1 NO_CALL 0,0 Sample_2 NO_CALL 0,0 Sample_3 NO_CALL 0,0 Sample_4 HOM_REF 1,0 Sample_5 HOM_REF 2,0 Sample_6 NO_CALL 0,0 Sample_7 HOM_REF 2,0 Sample_8 HOM_REF 3,0 Sample_9 HOM_REF 3,0 Sample_10 HOM_VAR 0,2 Sample_11 HOM_REF 2,0 Sample_12 NO_CALL 0,0 Sample_13NO_CALL 0,0
nucleotide representation in Biostar398854 output FASTA for the same SNP for these 13 samples:
Sample current output of Biostar398854 requested output of Biostar398854 Sample_1 a a Sample_2 a a Sample_3 a a Sample_4 a A Sample_5 a A Sample_6 a a Sample_7 a A Sample_8 a A Sample_9 a A Sample_10 T T Sample_11 a A Sample_12 a a Sample_13 a a