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Optimise the process
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Remove unix2dos
Remove gzipping the results
Add threads to bgzip
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@teepean
teepean authored Apr 16, 2019
1 parent e5102c0 commit e27cd0b
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Showing 2 changed files with 8 additions and 27 deletions.
Binary file modified BAM Analysis Kit.exe
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35 changes: 8 additions & 27 deletions console_bam.bat
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
@echo off
title BAM Analysis Kit 1.8
title BAM Analysis Kit 2.04

REM The MIT License (MIT)
REM Copyright © 2013-2015 Felix Immanuel
Expand All @@ -21,7 +21,7 @@ REM ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
REM OTHER DEALINGS IN THE SOFTWARE.

echo.
echo *** BAM Analysis Kit 1.8 ***
echo *** BAM Analysis Kit 2.04 ***
echo.
echo Project Website: http://www.y-str.org/2014/04/bam-analysis-kit.html
echo Tools Used: SAMTools, picard, bamtools, lobSTR, telseq, Cygwin, GATK, Java
Expand All @@ -33,7 +33,7 @@ if [%1]==[] goto NOPARAM
REM - start reporting versions..
bin\cygwin\bin\bash.exe -c "echo -n 'lobSTR Version: ';/bin/lobSTR --version"
bin\cygwin\bin\bash.exe -c "/bin/bedtools --version"
echo Samtools Version: 1.2
echo Samtools Version: 1.9
bin\cygwin\bin\bash.exe -c "echo -n 'Cygwin Version: ';/bin/uname -r"
bin\cygwin\bin\bash.exe -c "/bin/telseq --version|/bin/head -1"
bin\jre\bin\java -version 2^>^&1 ^| findstr /i version
Expand Down Expand Up @@ -321,7 +321,7 @@ echo Invoke the variant caller ...
IF "%%A" == "M" (

bin\cygwin\bin\bash.exe -c "./bin/jre/bin/java.exe %BAMKIT_JVM% -jar bin/gatk/GenomeAnalysisTK.jar -l INFO -R ref.fa -T HaplotypeCaller -I bam_sorted_realigned.bam -nct %BAMKIT_THREADS% -o bam_chr%%A.vcf"
bin\bow\bgzip.exe bam_chr%%A.vcf
bin\bow\bgzip.exe -@ %BAMKIT_THREADS% bam_chr%%A.vcf
bin\bow\tabix.exe bam_chr%%A.vcf.gz

echo Extracting mtDNA markers ..
Expand All @@ -342,8 +342,8 @@ echo Invoke the variant caller ...
IF EXIST bam_sorted_realigned.bam DEL /Q /F bam_sorted_realigned.bam
bin\cygwin\bin\bash.exe -c "./bin/jre/bin/java.exe %BAMKIT_JVM% -jar bin/gatk/GenomeAnalysisTK.jar -T IndelRealigner -maxPosMove 10 -R ref.fa -I bam_sorted.bam -targetIntervals bam.intervals -o bam_sorted_realigned.bam"
bin\cygwin\bin\bash.exe -c "./bin/jre/bin/java.exe %BAMKIT_JVM% -jar bin/gatk/GenomeAnalysisTK.jar -l INFO -R ref.fa -T HaplotypeCaller -I bam_sorted_realigned.bam -nct %BAMKIT_THREADS% -o bam_chr%%A.vcf"
bin\jre\bin\java.exe -jar bin\haplogrep\haplogrep-2.1.16.jar --in bam_chr%%A.vcf --format vcf --out out\mtDNA-haplogroup.txt
bin\bow\bgzip.exe bam_chr%%A.vcf
bin\jre\bin\java.exe -jar bin\haplogrep\haplogrep-2.1.16.jar --in bam_chr%%A.vcf --format vcf --out out\mtDNA-haplogroup-haplogrep.txt
bin\bow\bgzip.exe -@ %BAMKIT_THREADS% bam_chr%%A.vcf
bin\bow\tabix.exe bam_chr%%A.vcf.gz
bin\cygwin\bin\bash.exe -c "/bin/bcftools.exe query -f '%%CHROM\t%%POS\t[%%IUPACGT]\n' bam_chr%%A.vcf |/bin/sed 's/chr//g' | /bin/sed 's/\///g' > chr%%A.tab"
bin\cygwin\bin\bash.exe -c "/bin/bcftools.exe query -f '%%REF\t%%POS\t[%%IUPACGT]\n' bam_chr%%A.vcf |/bin/sed 's/chr//g' | /bin/sed 's/\///g'|/bin/awk '{if($3 ~ /^[ATGC]$/) printf $1\"\"$2\"\"$3\" \"}'|/bin/sed 's/\s$//g'|/bin/sed 's/\s/, /g' > out/RSRS_mtDNA.txt"
Expand All @@ -353,7 +353,7 @@ echo Invoke the variant caller ...

IF "%%A" == "Y" (
bin\cygwin\bin\bash.exe -c "./bin/jre/bin/java.exe %BAMKIT_JVM% -jar bin/gatk/GenomeAnalysisTK.jar -l INFO -R ref.fa -T UnifiedGenotyper -glm SNP -I bam_sorted_realigned.bam -rf BadCigar -nct %BAMKIT_THREADS% -o bam_chr%%A.vcf --output_mode EMIT_ALL_CONFIDENT_SITES"
bin\bow\bgzip.exe bam_chr%%A.vcf
bin\bow\bgzip.exe -@ %BAMKIT_THREADS% bam_chr%%A.vcf
bin\bow\tabix.exe bam_chr%%A.vcf.gz

echo Extracting Y-SNP markers ..
Expand All @@ -376,7 +376,7 @@ echo Invoke the variant caller ...

) ELSE (
bin\cygwin\bin\bash.exe -c "./bin/jre/bin/java.exe %BAMKIT_JVM% -jar bin/gatk/GenomeAnalysisTK.jar -l INFO -R ref.fa -T UnifiedGenotyper -glm SNP -I bam_sorted_realigned.bam -rf BadCigar -nct %BAMKIT_THREADS% -o bam_chr%%A.vcf --output_mode EMIT_ALL_CONFIDENT_SITES"
bin\bow\bgzip.exe bam_chr%%A.vcf
bin\bow\bgzip.exe -@ %BAMKIT_THREADS% bam_chr%%A.vcf
bin\bow\tabix.exe bam_chr%%A.vcf.gz
bin\cygwin\bin\bash.exe -c "/bin/bcftools.exe query -f '%%CHROM\t%%POS\t[%%TGT]\n' bam_chr%%A.vcf |/bin/sed 's/chr//g' > chr%%A.tab"
)
Expand Down Expand Up @@ -450,18 +450,6 @@ IF EXIST chrM.tmp DEL /Q /F chrM.tmp
)
)

IF EXIST out\RSRS_mtDNA.txt bin\cygwin\bin\bash.exe -c "/bin/unix2dos.exe ./out/RSRS_mtDNA.txt"
IF EXIST out\Variants_Y.txt bin\cygwin\bin\bash.exe -c "/bin/unix2dos.exe ./out/Variants_Y.txt"
IF EXIST out\Y-STR_Markers.txt bin\cygwin\bin\bash.exe -c "/bin/unix2dos.exe ./out/Y-STR_Markers.txt"
IF EXIST out\ISOGG_Y_Haplogroup.txt bin\cygwin\bin\bash.exe -c "/bin/unix2dos.exe ./out/ISOGG_Y_Haplogroup.txt"

bin\cygwin\bin\bash.exe -c "/bin/unix2dos.exe ./out/filtered-autosomal-o37-results.csv"
bin\cygwin\bin\bash.exe -c "/bin/unix2dos.exe ./out/filtered-x-chromosome-o37-results.csv"
bin\cygwin\bin\bash.exe -c "/bin/unix2dos.exe ./out/genome_complete.txt"
bin\cygwin\bin\bash.exe -c "/bin/unix2dos.exe ./out/genome_full_snps.txt"



IF "%TELOMERE%" == "yes" (
echo.
echo Processing Telomere ...
Expand Down Expand Up @@ -528,13 +516,6 @@ IF EXIST out\Admixture_Eurogenes_Report.html DEL /Q /F out\admix_result_eurogene

)


bin\cygwin\bin\bash.exe -c "/bin/gzip.exe ./out/filtered-autosomal-o37-results.csv"
bin\cygwin\bin\bash.exe -c "/bin/gzip.exe ./out/filtered-x-chromosome-o37-results.csv"
bin\cygwin\bin\bash.exe -c "/bin/gzip.exe ./out/genome_complete.txt"
bin\cygwin\bin\bash.exe -c "/bin/gzip.exe ./out/genome_full_snps.txt"


IF EXIST genotype.txt DEL /Q /F genotype.txt
IF EXIST snps.txt DEL /Q /F snps.txt
IF EXIST bam_complete_sorted.bam DEL /Q /F bam_complete_sorted.bam
Expand Down

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