#1
#File: 
TAF4_chr3_only.vcf.gz

#Description:
TAF4_chr3_only.vcf.gz contains variant calls for TAF4.bam in 3 chromosome.

#Command used:
bcftools mpileup -a 'FORMAT/DP,FORMAT/SP,FORMAT/AD,FORMAT/ADF,FORMAT/ADR,INFO/AD,INFO/ADR,INFO/ADF' -r chr3 -f wcg38.fa TAF4.sorted.bam | bcftools call -cv -p 0.05 | bcftools filter -i 'QUAL>=20 && FORMAT/DP>=5' -Oz -o TAF4_chr3_only.vcf.gz

#2
#File: 
TAF4_chr3_only.vcf.gz.tbi

#Description:
TAF4_chr3_only.vcf.gz.tbi is an index-file for TAF4_chr3_only.vcf.gz.

#Command used:
bcftools index -t TAF4_chr3_only.vcf.gz

#3
#File: 
chip.vcf.gz

#Description:
chip.vcf.gz contains variant calls for all ChIP-seq data in 3 chromosome.

#Command used:
bcftools mpileup -a 'FORMAT/DP,FORMAT/SP,FORMAT/AD,FORMAT/ADF,FORMAT/ADR,INFO/AD,INFO/ADR,INFO/ADF' -r chr3 -f ../wcg38.fa  input_iN_4-22_r1_L1_1.fq.gzinput_iN_4-22_r1_L1_2.fq.gz.bam  iN_4-22_Cre2_r1_L1_1.fq.gziN_4-22_Cre2_r1_L1_2.fq.gz.bam  iN_4-14_r1_L1_2.fq.gziN_4-14_r1_L1_1.fq.gz.bam  iN1-25_r1_L1_2.fq.gziN1-25_r1_L1_1.fq.gz.bam  iN_4-22_r2_L1_2.fq.gziN_4-22_r2_L1_1.fq.gz.bam  input_iN_14-8_r1_L1_2.fq.gzinput_iN_14-8_r1_L1_1.fq.gz.bam  input_iN_1-36_r2_L1_2.fq.gzinput_iN_1-36_r2_L1_1.fq.gz.bam  input_iN_1-36_r1_L1_2.fq.gzinput_iN_1-36_r1_L1_1.fq.gz.bam  delete/CB_wt_GGCTACCA_L1_1.fq.gzCB_wt_GGCTACCA_L1_2.fq.gz.bam  input_iN_14-10_r1_L1_1.fq.gzinput_iN_14-10_r1_L1_2.fq.gz.bam  input_iN_4-22_Cre2_r1_L1_1.fq.gzinput_iN_4-22_Cre2_r1_L1_2.fq.gz.bam  CB_wt_TAGCTTCA_L1_2.fq.gzCB_wt_TAGCTTCA_L1_1.fq.gz.bam  iN_1-36_r1_L1_2.fq.gziN_1-36_r1_L1_1.fq.gz.bam  input_iN_14-10_r2_L1_2.fq.gzinput_iN_14-10_r2_L1_1.fq.gz.bam  input_iN1-25_r1_L1_2.fq.gzinput_iN1-25_r1_L1_1.fq.gz.bam  CB_wt_GGCTACCA_L1_1.fq.gzCB_wt_GGCTACCA_L1_2.fq.gz.bam  iN_14-10_r1_L1_2.fq.gziN_14-10_r1_L1_1.fq.gz.bam  iN_4-22_r1_L1_1.fq.gziN_4-22_r1_L1_2.fq.gz.bam  input_iN_1-25_r2_L1_1.fq.gzinput_iN_1-25_r2_L1_2.fq.gz.bam  iN_4-22_Cre2_r2_L1_2.fq.gziN_4-22_Cre2_r2_L1_1.fq.gz.bam iN_1-36_r2_L1_1.fq.gziN_1-36_r2_L1_2.fq.gz.bam | bcftools call -cv -p 0.05 | bcftools filter -i 'QUAL>=20 && FORMAT/DP>=5' -Oz -o chip.vcf.gz

#4
#File: 
chip.vcf.gz.tbi

#Description:
chip.vcf.gz.tbi is an index-file for TAF4_chr3_only.vcf.gz.

#Command used:
bcftools index -t chip.vcf.gz

#5
#File: 
chip4.vcf.gz

#Description:
chip4.vcf.gz contains variant calls for ChIP-seq data of son.

#Command used:
bcftools mpileup -a 'FORMAT/DP,FORMAT/SP,FORMAT/AD,FORMAT/ADF,FORMAT/ADR,INFO/AD,INFO/ADR,INFO/ADF' -r chr3 -f ../wcg38.fa  input_iN_4-22_r1_L1_1.fq.gzinput_iN_4-22_r1_L1_2.fq.gz.bam  iN_4-22_Cre2_r1_L1_1.fq.gziN_4-22_Cre2_r1_L1_2.fq.gz.bam  iN_4-14_r1_L1_2.fq.gziN_4-14_r1_L1_1.fq.gz.bam  iN_4-22_r2_L1_2.fq.gziN_4-22_r2_L1_1.fq.gz.bam     input_iN_4-22_Cre2_r1_L1_1.fq.gzinput_iN_4-22_Cre2_r1_L1_2.fq.gz.bam   iN_4-22_r1_L1_1.fq.gziN_4-22_r1_L1_2.fq.gz.bam iN_4-22_Cre2_r2_L1_2.fq.gziN_4-22_Cre2_r2_L1_1.fq.gz.bam | bcftools call -cv -p 0.05 | bcftools filter -i 'QUAL>=20 && FORMAT/DP>=5' -Oz -o chip4.vcf.gz

#6
#File: 
chip4.vcf.gz.tbi

#Description:
chip4.vcf.gz.tbi is an index-file for chip4.vcf.gz.

#Command used:
bcftools index -t chip4.vcf.gz

#7
#File: 
chip14.vcf.gz

#Description:
chip14.vcf.gz contains variant calls for ChIP-seq data of father.

#Command used: 
bcftools mpileup -a 'FORMAT/DP,FORMAT/SP,FORMAT/AD,FORMAT/ADF,FORMAT/ADR,INFO/AD,INFO/ADR,INFO/ADF' -r chr3 -f ../wcg38.fa  input_iN_14-8_r1_L1_2.fq.gzinput_iN_14-8_r1_L1_1.fq.gz.bam  input_iN_14-10_r1_L1_1.fq.gzinput_iN_14-10_r1_L1_2.fq.gz.bam input_iN_14-10_r2_L1_2.fq.gzinput_iN_14-10_r2_L1_1.fq.gz.bam  iN_14-10_r1_L1_2.fq.gziN_14-10_r1_L1_1.fq.gz.bam | bcftools call -cv -p 0.05 | bcftools filter -i 'QUAL>=20 && FORMAT/DP>=5' -Oz -o chip14.vcf.gz

#8
#File: 
chip14.vcf.gz.tbi

#Description:
chip14.vcf.gz.tbi is an index-file for chip14.vcf.gz.

#Command used:
bcftools index -t chip14.vcf.gz

#9
#File: 
chip4_positive.vcf

#Description:
chip4_positive.vcf contains variant calls of the patient that definitely came from the father. (based on chip4.vcf)

#Command used:

#10
#File: 
chip4_positive_extended.vcf

#Description:
chip4_positive.vcf contains variant calls of the patient that definitely or probably came from the father (situation of 0/1 & 0/1 included). (based on chip4.vcf)

#Command used:

#11
#File: 
TAF4_positive.vcf

#Description:
chip4_positive.vcf contains variant calls of the patient that definitely came from the father. (based on TAF4_chr3_only.vcf)

#Command used:

#12
#File: 
TAF4_positive_extended.vcf

#Description:
chip4_positive.vcf contains variant calls of the patient that definitely or probably came from the father (situation of 0/1 & 0/1 included). (based on TAF4_chr3_only.vcf)

#Command used: